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Sample records for 3d geological structure

  1. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  2. Triangular framework mesh generation of 3D geological structure

    NASA Astrophysics Data System (ADS)

    Meng, Xianhai; Zhou, Kun; Li, Jigang; Yang, Qin

    2013-03-01

    The dynamic simulation of oil migration and accumulation is an important issue on the research of petroleum exploration, and it is a numerical simulation process with special requirement on the framework mesh of 3D geological models, which means that the mesh should have same geometry and topology relation near the intersected part of geological surfaces. In this paper, basing on the conforming Delaunay triangulation algorithm to construct mesh of individual geological stratum or fault, a novel link-Delaunay-triangulation method is presented to achieve the geometric and topological consistency in the intersected line between two surfaces, also with the analysis of termination of our algorithm. Finally, some examples of the geological framework mesh are provided and the experimental result proved that the algorithm's effectiveness in engineering practice.

  3. Self-Discovery of Structural Geology Concepts using Interactive 3D Visualization

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

    Mastering structural geology concepts that depend on understanding three-dimensional (3D) geometries and imagining relationships among unseen subsurface structures are fundamental skills for geologists. Traditionally these skills are developed first, through use of 2D drawings of 3D structures that can be difficult to decipher or 3D physical block models that show only a limited set of relationships on the surfaces of the blocks, followed by application and testing of concepts in field settings. We hypothesize that this learning process can be improved by providing repeated opportunities to evaluate and explore synthetic 3D structures using interactive 3D visualization software. We present laboratory modules designed for undergraduate structural geology curriculum using a self-discovery approach to teach concepts such as: the Rule of V’s, structure separation versus fault slip, and the more general dependence of structural exposure on surface topography. The laboratory modules are structured to allow students to discover and articulate each concept from observations of synthetic data both on traditional maps and using the volume visualization software 3DVisualizer. Modules lead students through exploration of data (e.g., a dipping layered structure exposed in ridge-valley topography or obliquely offset across a fault) by allowing them to interactively view (rotate, pan, zoom) the exposure of structures on topographic surfaces and to toggle on/off the full 3D structure as a transparent colored volume. This tool allows student to easily visually understand the relationships between, for example a dipping structure and its exposure on valley walls, as well as how the structure extends beneath the surface. Using this method gives students more opportunities to build a mental library of previously-seen relationships from which to draw-on when applying concepts in the field setting. These laboratory modules, the data and software are freely available from KeckCAVES.

  4. Imaging 3D geological structure of the Mygdonian basin (Northern Greece) with geological numerical modeling and geophysical methods.

    NASA Astrophysics Data System (ADS)

    Cédric, Guyonnet-Benaize; Fabrice, Hollender; Maria, Manakou; Alexandros, Savvaidis; Elena, Zargli; Cécile, Cornou; Nikolaos, Veranis; Dimitrios, Raptakis; Artemios, Atzemoglou; Pierre-Yves, Bard; Nikolaos, Theodulidis; Kyriazis, Pitilakis; Emmanuelle, Chaljub

    2013-04-01

    The Mygdonian basin, located 30 km E-NE close to Thessaloniki, is a typical active tectonic basin, trending E-NW, filled by sediments 200 to 400 m thick. This basin has been chosen as a European experimental site since 1993 (European Commission research projects - EUROSEISTEST). It has been investigated for experimental and theoretical studies on site effects. The Mygdonian basin is currently covered by a permanent seismological network and has been mainly characterized in 2D and 3D with geophysical and geotechnical studies (Bastani et al, 2011; Cadet and Savvaidis, 2011; Gurk et al, 2007; Manakou et al, 2007; Manakou et al, 2010; Pitilakis et al, 1999; Raptakis et al, 2000; Raptakis et al, 2005). All these studies allowed understanding the influence of geological structures and local site conditions on seismic site response. For these reasons, this site has been chosen for a verification exercise for numerical simulations in the framework of an ongoing international collaborative research project (Euroseistest Verification and Validation Project - E2VP). The verification phase has been made using a first 3D geophysical and geotechnical model (Manakou, 2007) about 5 km wide and 15 km long, centered on the Euroseistest site. After this verification phase, it has been decided to update, optimize and extend this model in order to obtain a more detailed model of the 3D geometry of the entire basin, especially the bedrock 3D geometry which can affect drastically the results of numerical simulations for site effect studies. In our study, we build a 3D geological model of the present-day structure of the entire Mygdonian basin. This "precise" model is 12 km wide, 65 km long and is 400 m deep in average. It has been built using geophysical, geotechnical and geological data. The database is heterogeneous and composed of hydrogeological boreholes, seismic refraction surveys, array microtremor measurements, electrical and geotechnical surveys. We propose an integrated

  5. The 3D geological model of the Eastern Romania tectonics and structure

    NASA Astrophysics Data System (ADS)

    Necula, Nicusor; Sorin Baciu, Dorin; Niculita, Mihai; Dumitriu, Tony-Cristian

    2016-04-01

    3D geologic modelling is a modern tool which allow the conceptualization of geologic relations in an interactive environment, strengthening the ability to understand and present tectonic and structural geologic models. We integrated the data available in the literature (wells, maps, cross-sections) for the geological structure of the Eastern Romania, comprising the Eastern Carpathians Orogen and its foreland. The subducting East European plate generated the Eastern Carphatians thrusts. Under the Eastern Carpathians, beside East European plate, the Tornquist-Teysseire zone is caught. East European Craton (Proterozoic), Scythian Platform (Paleozoic), North Dobrogean Orogen (Paleozoic) and Moesian Platform (Paleozoic), all neighbor Tornquist-Teysseire zone (Paleozoic), playing the role of foreland for the Eastern Carpathian Orogen. The Eastern Carphatians Orogen has two flysch belts, the Inner Carpathian called Dacides formed in Cretacic deformations and the Outer Carpathian called Moldavides and formed in Late Badenian to Sarmatian deformations. The modelling was performed in Midland Valley's Move software. The boundaries of all the structural units presented above were modelled, together with the faults which are represented on the various osurces used. The created 3D geological model is seen as a tool to better understand and represent the tectonic and structural model of the Eastern ROmania and will also allow a better quantification of the relations between geology and landforms in Eastern Romania.

  6. 3D stochastic inversion of potential field data using structural geologic constraints

    NASA Astrophysics Data System (ADS)

    Shamsipour, Pejman; Schetselaar, Ernst; Bellefleur, Gilles; Marcotte, Denis

    2014-12-01

    We introduce a new method to include structural orientation constraints into potential field inversion using a stochastic framework. The method considers known geological interfaces and planar orientation data such as stratification estimated from seismic surveys or drill hole information. Integrating prior geological information into inversion methods can effectively reduce ambiguity and improve inversion results. The presented approach uses cokriging prediction with derivatives. The method is applied to two synthetic models to demonstrate its suitability for 3D inversion of potential field data. The method is also applied to the inversion of gravity data collected over the Lalor volcanogenic massive sulfide deposit at Snow Lake, Central Manitoba, Canada. The results show that using a structurally-constrained inversion leads to a better-resolved solution.

  7. How Students and Field Geologists Reason in Integrating Spatial Observations from Outcrops to Visualize a 3-D Geological Structure

    ERIC Educational Resources Information Center

    Kastens, Kim A.; Agrawal, Shruti; Liben, Lynn S.

    2009-01-01

    Geologists and undergraduate students observed eight artificial "rock outcrops" in a realistically scaled field area, and then tried to envision a geological structure that might plausibly be formed by the layered rocks in the set of outcrops. Students were videotaped as they selected which of fourteen 3-D models they thought best represented the…

  8. 3D-geological structures with digital elevation models using GPU programming

    NASA Astrophysics Data System (ADS)

    Mateo Lázaro, Jesús; Sánchez Navarro, José Ángel; García Gil, Alejandro; Edo Romero, Vanesa

    2014-09-01

    We present an application that visualises three-dimensional geological structures with digital terrain models. The three-dimensional structures are displayed as their intersections with two-dimensional surfaces that may be defined analytically (e.g., sections) or with grid meshes in the case of irregular surfaces such as the digital terrain models. The process begins with classic techniques of terrain visualisation using hypsometric shading with textures. Then, geometric transformations that are easily conceived and programmed are added, thus representing the three-dimensional structures with their location and orientation. Functions of three variables are used to define the geological structures, and data from digital terrain models are used as one of the variables. This provides a simple source code and results in a short calculation time. Additionally, the process of generating new textures can be performed by a Graphics Processing Unit (GPU), thereby making real-time processing very effective and providing the possibility of displaying the simulation of geological structures in motion.

  9. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O.; Samson, P.; Segonds, D.

    1996-12-31

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological {open_quotes}objects{close_quotes} with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  10. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O. ); Samson, P. ); Segonds, D. )

    1996-01-01

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological [open quotes]objects[close quotes] with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  11. Interactive editing of 3D geological structures and tectonic history sketching via a rigid element method

    NASA Astrophysics Data System (ADS)

    Laurent, Gautier; Caumon, Guillaume; Jessell, Mark

    2015-01-01

    Numerical models of geological structures are generally built with a geometrical approach, which lacks an explicit representation of the deformation history and may lead to incompatible structures. We advocate that the deformation history should be investigated and represented from the very first steps of the modelling process, provided that a series of rapid, interactive or automated, deformation tools are available for local editing, forward modelling and restoration. In this paper, we define the specifications of such tools and emphasise the need for rapidity and robustness. We briefly review the different applications of deformation tools in geomodelling and the existing deformation algorithms. We select a deformation algorithm based on rigid elements, first presented in the Computer Graphics community, which we refer to as Reed. It is able to rapidly deform any kind of geometrical object, including points, lines or volumes, with an approximated mechanical behaviour. The objects to be deformed are embedded in rigid cells whose displacement is optimised by minimising a global cost function with respect to displacement boundary conditions. This cost function measures the difference in displacement between neighbouring elements. The embedded objects are then deformed based on their original position with respect to the rigid elements. We present the basis of our implementation of this algorithm and highlight its ability to fulfil the specifications we defined. Its application to geomodelling specific problems is illustrated through the construction of a synthetic structural model of multiply deformed layers with a forward modelling approach. A special boundary condition adapted to restore large folds is also presented and applied to the large anticline of Han-sur-Lesse, Belgium, which demonstrates the ability of this method to efficiently perform a volumetric restoration without global projections.

  12. Visualization of 3D Geological Data using COLLADA and KML

    NASA Astrophysics Data System (ADS)

    Choi, Yosoon; Um, Jeong-Gi; Park, Myong-Ho

    2013-04-01

    This study presents a method to visualize 3D geological data using COLLAborative Design Activity(COLLADA, an open standard XML schema for establishing interactive 3D applications) and Keyhole Markup Language(KML, the XML-based scripting language of Google Earth).We used COLLADA files to represent different 3D geological data such as borehole, fence section, surface-based 3D volume and 3D grid by triangle meshes(a set of triangles connected by their common edges or corners). The COLLADA files were imported into the 3D render window of Google Earth using KML codes. An application to the Grosmont formation in Alberta, Canada showed that the combination of COLLADA and KML enables Google Earth to visualize 3D geological structures and properties.

  13. Visualization of 3D Geological Models on Google Earth

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Um, J.; Park, M.

    2013-05-01

    Google Earth combines satellite imagery, aerial photography, thematic maps and various data sets to make a three-dimensional (3D) interactive image of the world. Currently, Google Earth is a popular visualization tool in a variety of fields and plays an increasingly important role not only for private users in daily life, but also for scientists, practitioners, policymakers and stakeholders in research and application. In this study, a method to visualize 3D geological models on Google Earth is presented. COLLAborative Design Activity (COLLADA, an open standard XML schema for establishing interactive 3D applications) was used to represent different 3D geological models such as borehole, fence section, surface-based 3D volume and 3D grid by triangle meshes (a set of triangles connected by their common edges or corners). In addition, we designed Keyhole Markup Language (KML, the XML-based scripting language of Google Earth) codes to import the COLLADA files into the 3D render window of Google Earth. The method was applied to the Grosmont formation in Alberta, Canada. The application showed that the combination of COLLADA and KML enables Google Earth to effectively visualize 3D geological structures and properties.; Visualization of the (a) boreholes, (b) fence sections, (c) 3D volume model and (d) 3D grid model of Grossmont formation on Google Earth

  14. Fallon FORGE 3D Geologic Model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

    An x,y,z scattered data file for the 3D geologic model of the Fallon FORGE site. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  15. iBem3D, a three-dimensional iterative boundary element method using angular dislocations for modeling geologic structures

    NASA Astrophysics Data System (ADS)

    Maerten, F.; Maerten, L.; Pollard, D. D.

    2014-11-01

    Most analytical solutions to engineering or geological problems are limited to simple geometries. For example, analytical solutions have been found to solve for stresses around a circular hole in a plate. To solve more complex problems, mathematicians and engineers have developed powerful computer-aided numerical methods, which can be categorized into two main types: differential methods and integral methods. The finite element method (FEM) is a differential method that was developed in the 1950s and is one of the most commonly used numerical methods today. Since its development, other differential methods, including the boundary element method (BEM), have been developed to solve different types of problems. The purpose of this paper is to describe iBem3D, formally called Poly3D, a C++ and modular 3D boundary element computer program based on the theory of angular dislocations for modeling three-dimensional (3D) discontinuities in an elastic, heterogeneous, isotropic whole- or half-space. After 20 years and more than 150 scientific publications, we present in detail the formulation behind this method, its enhancements over the years as well as some important applications in several domains of the geosciences. The main advantage of using this formulation, for describing geological objects such as faults, resides in the possibility of modeling complex geometries without gaps and overlaps between adjacent triangular dislocation elements, which is a significant shortcoming for models using rectangular dislocation elements. Reliability, speed, simplicity, and accuracy are enhanced in the latest version of the computer code. Industrial applications include subseismic fault modeling, fractured reservoir modeling, interpretation and validation of fault connectivity and reservoir compartmentalization, depleted area and fault reactivation, and pressurized wellbore stability. Academic applications include earthquake and volcano monitoring, hazard mitigation, and slope

  16. Stereo 3-D Imagery Uses for Definition of Geologic Structures and Geomorphic Features (Anaglyph colored glasses employed)

    NASA Astrophysics Data System (ADS)

    Hicks, B. G.; Fuente, J. D.

    2008-12-01

    Recently completed projects incorporating TopoMorpher* digital images as adjuncts to commonly employed tools has emphasized the distinct advantage gained with STEREO 3-D DIGITAL IMAGERY. By manipulating scale, relief (four types of digital shading), sun angle, direction of viewing and tilt of scene, etc. -- to produce differing views of the same terrain -- aids in identifying, tracing, and interpreting ground surface anomalies. *TopoMorpher is a digital software product of Eighteen Software (18 software.com). The advantage of Stereo 3-D views combined with digital removal of vegetation which blocked interpretation (commonly called 'bare earth/naked' views) cannot be over-emphasized. The TopoMorpher program creates scenes transferable to disk for printing at any size. Included is with computer projector which allows large display and discussion ease for groups. The examples include (1) fault systems for targeting water well locations in bedrock and (2) delineation of debris slide and avalanche terrain. Combining geologic mapping and spring locations with Stereo 3-D TopoMorpher tracing of fault lineaments has allowed targeting of water well drilling sites. Selection of geophysical study areas for well siting has been simplified. Stereo 3-D TopoMorpher has a specific "relief/terrain setting" to define potential failure sites by producing detailed colored slope maps keyed to field-data derived parameters. Posters display individual project images and large scale overviews for identifying unusual major terrain features. Images at scales using 10 and 30 meter digital data as well as Lidar (< 1 meter) will be shown.

  17. 3D Geologic Model of the San Diego Area

    NASA Astrophysics Data System (ADS)

    Danskin, W. R.; Cromwell, G.; Glockhoff, C.; Martin, D.

    2015-12-01

    Prior geologic studies of the San Diego area, including northern Baja California, Mexico, focused on site investigations, characterization of rock formations, or earthquake hazards. No comprehensive, quantitative model characterizing the three-dimensional (3D) geology of the entire area has been developed. The lack of such a model limits understanding of large-scale processes, such as development of ancient landforms, and groundwater movement and availability. To evaluate these regional processes, the United States Geological Survey (USGS) conducted a study to better understand the geologic structure of the San Diego area. A cornerstone of this study is the installation and analysis of 77 wells at 12 multiple-depth monitoring-well sites. Geologic information from these wells was combined with lithologic data from 81 oil exploration wells and municipal and private water wells, gravity and seismic interpretations, and paleontological interpretations. These data were analyzed in conjunction with geologic maps and digital elevation models to develop a 3D geologic model of the San Diego area, in particular of the San Diego embayment. Existing interpretations of regional surficial geology, faulting, and tectonic history provided the framework for this model, which was refined by independent evaluation of subsurface geology. Geologic formations were simplified into five sedimentary units (Quaternary, Plio-Pleistocene, Oligocene, Eocene and Cretaceous ages), and one basal crystalline unit (primarily Cretaceous and Jurassic). Complex fault systems are represented in the model by ten fault strands that maintain overall displacement. The 3D geologic model corroborates existing geologic concepts of the San Diego area, refines the extent of subsurface geology, and allows users to holistically evaluate subsurface structures and regional hydrogeology.

  18. Teaching the geological subsurface with 3D models

    NASA Astrophysics Data System (ADS)

    Thorpe, Steve; Ward, Emma

    2014-05-01

    3D geological models have great potential as a resource when teaching geological concepts as it allows the student to visualise and interrogate UK geology. They are especially useful when dealing with the conversion of 2D field, map and GIS outputs into three dimensional geological units, which is a common problem for many students. Today's earth science students use a variety of skills and processes during their learning experience including spatial thinking, image construction, detecting patterns, making predictions and deducing the orientation of themselves. 3D geological models can reinforce spatial thinking strategies and encourage students to think about processes and properties, in turn helping the student to recognise pre-learnt geological principles in the field and to convert what they see at the surface into a picture of what is going on at depth. The British Geological Survey (BGS) has been producing digital 3D geological models for over 10 years. The models produced are revolutionising the working practices, data standards and products of the BGS. Sharing our geoscience information with academia is highlighted throughout the BGS strategy as is instilling practical skills in future geoscience professionals, such as model building and interpretation. In 2009 a project was launched to investigate the potential of the models as a teaching resource. The study included justifying if and how the models help students to learn, how models have been used historically, and how other forms of modelling are being used today. BGS now produce 3D geological models for use by anyone teaching or learning geoscience. They incorporate educational strategies that will develop geospatial skills and alleviate potential problems that some students experience. They are contained within contemporary case studies and show standard geological concepts, structures, sedimentary rocks, cross sections and field techniques. 3D geological models of the Isle of Wight and Ingleborough

  19. 3D Geological modelling - towards a European level infrastructure

    NASA Astrophysics Data System (ADS)

    Lee, Kathryn A.; van der Krogt, Rob; Busschers, Freek S.

    2013-04-01

    The joint European Geological Surveys are preparing the ground for a "European Geological Data Infrastructure" (EGDI), under the framework of the FP7-project EGDI-Scope. This scoping study, started in June 2012, for a pan-European e-Infrastructure is based on the successes of earlier joint projects including 'OneGeology-Europe' and aims to provide the backbone for serving interoperable, geological data currently held by European Geological Surveys. Also data from past, ongoing and future European projects will be incorporated. The scope will include an investigation of the functional and technical requirements for serving 3D geological models and will look to research the potential for providing a framework to integrate models at different scales, and form a structure for enabling the development of new and innovative model delivery mechanisms. The EGDI-scope project encourages pan-European inter-disciplinary collaboration between all European Geological Surveys. It aims to enhance emerging web based technologies that will facilitate the delivery of geological data to user communities involved in European policy making and international industry, but also to geoscientific research communities and the general public. Therefore, stakeholder input and communication is imperative to the success, as is the collaboration with all the Geological Surveys of Europe. The most important functional and technical requirements for delivery of such information at pan-European level will be derived from exchanges with relevant European stakeholder representatives and providers of geological data. For handling and delivering 3D geological model data the project will need to address a number of strategic issues: • Which are the most important issues and queries for the relevant stakeholders, requiring 3D geological models? How can this be translated to functional requirements for development and design of an integrated European application? • How to handle the very large

  20. 3D Geological Model for "LUSI" - a Deep Geothermal System

    NASA Astrophysics Data System (ADS)

    Sohrabi, Reza; Jansen, Gunnar; Mazzini, Adriano; Galvan, Boris; Miller, Stephen A.

    2016-04-01

    Geothermal applications require the correct simulation of flow and heat transport processes in porous media, and many of these media, like deep volcanic hydrothermal systems, host a certain degree of fracturing. This work aims to understand the heat and fluid transport within a new-born sedimentary hosted geothermal system, termed Lusi, that began erupting in 2006 in East Java, Indonesia. Our goal is to develop conceptual and numerical models capable of simulating multiphase flow within large-scale fractured reservoirs such as the Lusi region, with fractures of arbitrary size, orientation and shape. Additionally, these models can also address a number of other applications, including Enhanced Geothermal Systems (EGS), CO2 sequestration (Carbon Capture and Storage CCS), and nuclear waste isolation. Fractured systems are ubiquitous, with a wide-range of lengths and scales, making difficult the development of a general model that can easily handle this complexity. We are developing a flexible continuum approach with an efficient, accurate numerical simulator based on an appropriate 3D geological model representing the structure of the deep geothermal reservoir. Using previous studies, borehole information and seismic data obtained in the framework of the Lusi Lab project (ERC grant n°308126), we present here the first 3D geological model of Lusi. This model is calculated using implicit 3D potential field or multi-potential fields, depending on the geological context and complexity. This method is based on geological pile containing the geological history of the area and relationship between geological bodies allowing automatic computation of intersections and volume reconstruction. Based on the 3D geological model, we developed a new mesh algorithm to create hexahedral octree meshes to transfer the structural geological information for 3D numerical simulations to quantify Thermal-Hydraulic-Mechanical-Chemical (THMC) physical processes.

  1. 3D Reconstruction of geological structures based on remote sensing data: example from Anaran anticline, Lurestan province, Zagros folds and thrust belt, Iran.

    NASA Astrophysics Data System (ADS)

    Snidero, M.; Amilibia, A.; Gratacos, O.; Muñoz, J. A.

    2009-04-01

    This work presents a methodological workflow for the 3D reconstruction of geological surfaces at regional scale, based on remote sensing data and geological maps. This workflow has been tested on the reconstruction of the Anaran anticline, located in the Zagros Fold and Thrust belt mountain front. The used remote sensing data-set is a combination of Aster and Spot images as well as a high resolution digital elevation model. A consistent spatial positioning of the complete data-set in a 3D environment is necessary to obtain satisfactory results during the reconstruction. The Aster images have been processed by the Optimum Index Factor (OIF) technique, in order to facilitate the geological mapping. By pansharpening of the resulting Aster image with the SPOT panchromatic one we obtain the final high-resolution image used during the 3D mapping. Structural data (dip data) has been acquired through the analysis of the 3D mapped geological traces. Structural analysis of the resulting data-set allows us to divide the structure in different cylindrical domains. Related plunge lines orientation has been used to project data along the structure, covering areas with little or no information. Once a satisfactory dataset has been acquired, we reconstruct a selected horizon following the dip-domain concept. By manual editing, the obtained surfaces have been adjusted to the mapped geological limits as well as to the modeled faults. With the implementation of the Discrete Smooth Interpolation (DSI) algorithm, the final surfaces have been reconstructed along the anticline. Up to date the results demonstrate that the proposed methodology is a powerful tool for 3D reconstruction of geological surfaces when working with remote sensing data, in very inaccessible areas (eg. Iran, China, Africa). It is especially useful in semiarid regions where the structure strongly controls the topography. The reconstructed surfaces clearly show the geometry in the different sectors of the structure

  2. 3D Detection, Quantification and Correlation of Slope Failures with Geologic Structure in the Mont Blanc massif

    NASA Astrophysics Data System (ADS)

    Allan, Mark; Dunning, Stuart; Lim, Michael; Woodward, John

    2016-04-01

    A thorough understanding of supply from landslides and knowledge of their spatial distribution is of fundamental importance to high-mountain sediment budgets. Advances in 3D data acquisition techniques are heralding new opportunities to create high-resolution topographic models to aid our understanding of landscape change through time. In this study, we use a Structure-from-Motion Multi-View Stereo (SfM-MVS) approach to detect and quantify slope failures at selected sites in the Mont Blanc massif. Past and present glaciations along with its topographical characteristics have resulted in a high rate of geomorphological activity within the range. Data for SfM-MVS processing were captured across variable temporal scales to examine short-term (daily), seasonal and annual change from terrestrial, Unmanned Aerial Vehicle (UAV) and helicopter perspectives. Variable spatial scales were also examined ranging from small focussed slopes (~0.01 km2) to large valley-scale surveys (~3 km2). Alignment and registration were conducted using a series of Ground Control Points (GCPs) across the surveyed slope at various heights and slope aspects. GCPs were also used to optimise data and reduce non-linear distortions. 3D differencing was performed using a multiscale model-to-model comparison algorithm (M3C2) which uses variable thresholding across each slope based on local surface roughness and model alignment quality. Detected change was correlated with local slope structure and 3D discontinuity analysis was undertaken using a plane-detection and clustering approach (DSE). Computation of joint spacing was performed using the classified data and normal distances. Structural analysis allowed us to assign a Slope Mass Rating (SMR) and assess the stability of each slope relative to the detected change and determine likely failure modes. We demonstrate an entirely 3D workflow which preserves the complexity of alpine slope topography to compute volumetric loss using a variable threshold. A

  3. Additional geological insight brought by 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Milton, J.

    2002-12-01

    3-D seismic data allows geo-scientists to study the earth at a level that is much more detailed than ever. It is shown in this case study that 3-D seismic can not only be used to identify different types of oil/gas reservoirs, significantly reduce the risk of misinterpretation, but also help to understand geological history and establish paleogeography at different geological times. In the study of Southeast Maricopa Seismic Survey in southern San Joaquin Valley, two types of potential hydrocarbon traps are interpreted: stratigraphical traps due to turbidite channels, and structural traps due to faulting. The distinctive characteristics of two types of channels indicate different depositional environments. With 3-D visualization tools, it is found that localized faults had been leaking during certain geological times, resulting in structural traps of oil/gas. A geological history of the local area can be estimated by building a series of pseudo-paleogeographic maps using 3-D seismic data, which further reconfirms the existence of different depositional systems indicated by two distinctive types of channels.

  4. Summary on Several Key Techniques in 3D Geological Modeling

    PubMed Central

    2014-01-01

    Several key techniques in 3D geological modeling including planar mesh generation, spatial interpolation, and surface intersection are summarized in this paper. Note that these techniques are generic and widely used in various applications but play a key role in 3D geological modeling. There are two essential procedures in 3D geological modeling: the first is the simulation of geological interfaces using geometric surfaces and the second is the building of geological objects by means of various geometric computations such as the intersection of surfaces. Discrete geometric surfaces that represent geological interfaces can be generated by creating planar meshes first and then spatially interpolating; those surfaces intersect and then form volumes that represent three-dimensional geological objects such as rock bodies. In this paper, the most commonly used algorithms of the key techniques in 3D geological modeling are summarized. PMID:24772029

  5. Development of 3D Geological Structure Analysis Method Using Multi-geophysical Data: Application to Hwasan Caldera in Korea

    NASA Astrophysics Data System (ADS)

    Park, G.; Yang, J.; Yi, M.; Kim, J.; Kwon, B.

    2011-12-01

    Multi-geophysical surveys were carried out around the Hwasan caldera at the Euisung Sub-basin in Korea. To overcome the limitations of survey resolutions of previous studies, 510 points of gravity and 32 points of magnetotelluric (MT) data were obtained. To analyze three-dimensional density and resistivity models, gravity and MT inversions were carried out using Marquardt-Levenberg method and WSINV3DMT code, respectively. To carry out the objective structure analysis of multi-parametric geophysical data, a new classification technique, Structure Index (SI) method, was proposed. SI method consists of Type Angle (TA) and Type Intensity (TI) values. It is one of the projection techniques similar to the universal transverse Mercator (UTM) projection, and a mathematical method of showing the patterns of correlation and abnormalness of physical property values by TA and TI values. TA values indicate the correlation patterns of normalized data sets and TI values show the levels of the abnormalness of physical property values. For the processing, the density and resistivity values were estimated at the same nodes using kriging methods through S-GeMS based on GSLIB. Base on the results of the SI processing, all classified nodes were plotted and visualized in 3-dimensional space as shown in Fig. 1. The analyzed results of SI method using gravity and MT data match well with those of the previous researches, including the geologic map. First, the intrusive igneous rocks, which have high density and resistivity values, were analyzed according to the ring fault and intrusive igneous area at the north-east side of the Hwasan caldera. Second, the pyroclastic rocks at the center of the caldera, which is extended to a depth of around 1 km with low density and resistivity values, were imaged. The basement structure, which has a relatively low resistivity and high density at a depth of 5 km was also inferred by integration analysis. This method makes it possible to classify and three

  6. High precision analysis of an embryonic extensional fault-related fold using 3D orthorectified virtual outcrops: The viewpoint importance in structural geology

    NASA Astrophysics Data System (ADS)

    Tavani, Stefano; Corradetti, Amerigo; Billi, Andrea

    2016-05-01

    Image-based 3D modeling has recently opened the way to the use of virtual outcrop models in geology. An intriguing application of this method involves the production of orthorectified images of outcrops using almost any user-defined point of view, so that photorealistic cross-sections suitable for numerous geological purposes and measurements can be easily generated. These purposes include the accurate quantitative analysis of fault-fold relationships starting from imperfectly oriented and partly inaccessible real outcrops. We applied the method of image-based 3D modeling and orthorectification to a case study from the northern Apennines, Italy, where an incipient extensional fault affecting well-layered limestones is exposed on a 10-m-high barely accessible cliff. Through a few simple steps, we constructed a high-quality image-based 3D model of the outcrop. In the model, we made a series of measurements including fault and bedding attitudes, which allowed us to derive the bedding-fault intersection direction. We then used this direction as viewpoint to obtain a distortion-free photorealistic cross-section, on which we measured bed dips and thicknesses as well as fault stratigraphic separations. These measurements allowed us to identify a slight difference (i.e. only 0.5°) between the hangingwall and footwall cutoff angles. We show that the hangingwall strain required to compensate the upward-decreasing displacement of the fault was accommodated by this 0.5° rotation (i.e. folding) and coeval 0.8% thickening of strata in the hangingwall relatively to footwall strata. This evidence is consistent with trishear fault-propagation folding. Our results emphasize the viewpoint importance in structural geology and therefore the potential of using orthorectified virtual outcrops.

  7. Deducing the subsurface geological conditions and structural framework of the NE Gulf of Suez area, using 2-D and 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Zahra, Hesham Shaker; Nakhla, Adel Mokhles

    2015-06-01

    An interpretation of the seismic data of Ras Budran and Abu Zenima oil fields, northern central Gulf of Suez, is carried out to evaluate its subsurface tectonic setting. The structural configuration, as well as the tectonic features of the concerned area is criticized through the study of 2D and 3D seismic data interpretation with the available geological data, in which the geo-seismic depth maps for the main interesting levels (Kareem, Nukhul, Matulla, Raha and Nubia Formations) are depicted. Such maps reflect that, the Miocene structure of Ras Budran area is a nearly NE-SW trending anticlinal feature, which broken into several panels by a set of NWSE and NE-SW trending faults. The Pre-Miocene structure of the studied area is very complex, where Ras Budran area consists of step faults down stepping to the south and southwest, which have been subjected to cross faults of NE-SW trend with lateral and vertical displacements.

  8. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  9. 3D PDF - a means of public access to geological 3D - objects, using the example of GTA3D

    NASA Astrophysics Data System (ADS)

    Slaby, Mark-Fabian; Reimann, Rüdiger

    2013-04-01

    In geology, 3D modeling has become very important. In the past, two-dimensional data such as isolines, drilling profiles, or cross-sections based on those, were used to illustrate the subsurface geology, whereas now, we can create complex digital 3D models. These models are produced with special software, such as GOCAD ®. The models can be viewed, only through the software used to create them, or through viewers available for free. The platform-independent PDF (Portable Document Format), enforced by Adobe, has found a wide distribution. This format has constantly evolved over time. Meanwhile, it is possible to display CAD data in an Adobe 3D PDF file with the free Adobe Reader (version 7). In a 3D PDF, a 3D model is freely rotatable and can be assembled from a plurality of objects, which can thus be viewed from all directions on their own. In addition, it is possible to create moveable cross-sections (profiles), and to assign transparency to the objects. Based on industry-standard CAD software, 3D PDFs can be generated from a large number of formats, or even be exported directly from this software. In geoinformatics, different approaches to creating 3D PDFs exist. The intent of the Authority for Mining, Energy and Geology to allow free access to the models of the Geotectonic Atlas (GTA3D), could not be realized with standard software solutions. A specially designed code converts the 3D objects to VRML (Virtual Reality Modeling Language). VRML is one of the few formats that allow using image files (maps) as textures, and to represent colors and shapes correctly. The files were merged in Acrobat X Pro, and a 3D PDF was generated subsequently. A topographic map, a display of geographic directions and horizontal and vertical scales help to facilitate the use.

  10. 3-D seismic imaging of complex geologies

    SciTech Connect

    Womble, D.E.; Dosanjh, S.S.; VanDyke, J.P.; Oldfield, R.A.; Greenberg, D.S.

    1995-02-01

    We present three codes for the Intel Paragon that address the problem of three-dimensional seismic imaging of complex geologies. The first code models acoustic wave propagation and can be used to generate data sets to calibrate and validate seismic imaging codes. This code reported the fastest timings for acoustic wave propagation codes at a recent SEG (Society of Exploration Geophysicists) meeting. The second code implements a Kirchhoff method for pre-stack depth migration. Development of this code is almost complete, and preliminary results are presented. The third code implements a wave equation approach to seismic migration and is a Paragon implementation of a code from the ARCO Seismic Benchmark Suite.

  11. 3D Geologic Model of the Southern Great Basin

    NASA Astrophysics Data System (ADS)

    Wagoner, J. L.; Myers, S. C.

    2006-12-01

    We have constructed a regional 3D geologic model of the southern Great Basin, in support of a seismic wave propagation investigation of the 1993 Nonproliferation Experiment (NPE) at the Nevada Test Site (NTS). The model is centered on the NPE and spans longitude -119.5° to -112.6°, latitude 34.5° to 39.8°, and a depth from the surface to 150 km below sea level. Hence, the model includes the southern half of Nevada, as well as parts of eastern California, western Utah, and a portion of northwestern Arizona. The upper crust is constrained by geologic and geophysical studies, and the lower crust and upper mantle are constrained by geophysical studies. The upper crustal geologic units are Quaternary basin fill, Tertiary deposits, pre-Tertiary deposits, intrusive rocks, and calderas. The lower crust and upper mantle are parameterized with 8 layers, including the Moho. Detailed geologic data, including surface maps, borehole data, and geophysical surveys, were used to define the geology at the NTS. Digital geologic outcrop data were available for both Nevada and Arizona, whereas we scanned and hand digitized geologic maps for California and Utah. Published gravity data (2km spacing) were used to determine the thickness of the Cenozoic deposits and constrain the depth of the basins. The free surface is based on a 10m lateral resolution DEM at the NTS and a 90m resolution DEM elsewhere. The gross geophysical structure of the crust and upper mantle is taken from regional surface-wave studies. Variations in crustal thickness are based on receiver function analysis and a compilation of reflection/refraction studies. We used the Earthvision (Dynamic Graphics, Inc.) software to integrate the geologic and geophysical information into a model of x,y,z,p nodes, where p is an integer index representing the geologic unit. For regional seismic simulations we convert this realistic geologic model into elastic parameters. Upper crustal units are treated as seismically homogeneous

  12. Potential field Modeling of the 3-D Geologic Structure of the San Andreas Fault Observatory at Depth (SAFOD) at Parkfield, California

    NASA Astrophysics Data System (ADS)

    McPhee, D. K.

    2003-12-01

    Gravity and magnetic data, along with other geophysical and geological constraints, are used to develop 2-D models that we use to characterize the 3-D geological structure of the San Andreas fault (SAF) zone in the vicinity of SAFOD near Parkfield, CA. The gravity data, reduced to isostatic anomalies, comprise a compilation of three different data sets with a maximum of 1.6 km grid spacing for the scattered data and closely spaced ( ˜40 m) stations along one SW-NE profile crossing the SAFOD pilot hole. Aeromagnetic data were flown at a nominal 300 m above the terrain along SW-NE flight lines perpendicular to the San Andreas Fault. Data were recorded at ˜50 m spacing along flight lines approximately 800 m apart. Ground magnetic data recorded every 5 m along lines ˜300 m apart cover a 3 x 5 km area surrounding the SAFOD pilot hole. Previous modeling showed that magnetic granitic basement rocks southwest of the SAF are divided by an inferred steep fault sub-parallel to the SAF. We compute 2-D crustal models along 5 km-long southwest-northeast profiles, one of which extends through the SAFOD pilot hole near and along the high-resolution seismic refraction/reflection survey completed in 1998 (Catchings et al., 2002). Our models are constrained by pilot hole measurements, where we see a boundary between sediment and granitic basement at ˜770 m and an order of magnitude increase in magnetic susceptibility at ˜1400 m, possibly the same depth at which the SW dipping Buzzard Canyon Fault intersects the pilot hole. Regional gravity, magnetic and geologic data indicate two very distinct basement blocks separated by a steeply dipping SAF. The shallowly dipping sedimentary section SW of the SAF coincides with the low velocity zone observed with seismic measurements. Shallow slivers of magnetic sandstone on the NE side of the SAF explain higher frequency features in the magnetic data. In addition, we show a flat lying, tabular body of serpentinite sandwiched between 2 blocks

  13. A web-based 3D geological information visualization system

    NASA Astrophysics Data System (ADS)

    Song, Renbo; Jiang, Nan

    2013-03-01

    Construction of 3D geological visualization system has attracted much more concern in GIS, computer modeling, simulation and visualization fields. It not only can effectively help geological interpretation and analysis work, but also can it can help leveling up geosciences professional education. In this paper, an applet-based method was introduced for developing a web-based 3D geological information visualization system. The main aims of this paper are to explore a rapid and low-cost development method for constructing a web-based 3D geological system. First, the borehole data stored in Excel spreadsheets was extracted and then stored in SQLSERVER database of a web server. Second, the JDBC data access component was utilized for providing the capability of access the database. Third, the user interface was implemented with applet component embedded in JSP page and the 3D viewing and querying functions were implemented with PickCanvas of Java3D. Last, the borehole data acquired from geological survey were used for test the system, and the test results has shown that related methods of this paper have a certain application values.

  14. Geological mapping goes 3-D in response to societal needs

    USGS Publications Warehouse

    Thorleifson, H.; Berg, R.C.; Russell, H.A.J.

    2010-01-01

    The transition to 3-D mapping has been made possible by technological advances in digital cartography, GIS, data storage, analysis, and visualization. Despite various challenges, technological advancements facilitated a gradual transition from 2-D maps to 2.5-D draped maps to 3-D geological mapping, supported by digital spatial and relational databases that can be interrogated horizontally or vertically and viewed interactively. Challenges associated with data collection, human resources, and information management are daunting due to their resource and training requirements. The exchange of strategies at the workshops has highlighted the use of basin analysis to develop a process-based predictive knowledge framework that facilitates data integration. Three-dimensional geological information meets a public demand that fills in the blanks left by conventional 2-D mapping. Two-dimensional mapping will, however, remain the standard method for extensive areas of complex geology, particularly where deformed igneous and metamorphic rocks defy attempts at 3-D depiction.

  15. 3D Geological Model of Nihe ore deposit Constrained by Gravity and Magnetic Modeling

    NASA Astrophysics Data System (ADS)

    Qi, Guang; Yan, Jiayong; Lv, Qingtan; Zhao, Jinhua

    2016-04-01

    We present a case study on using integrated geologic model in mineral exploration at depth. Nihe ore deposit in Anhui Province, is deep hidden ore deposit which was discovered in recent years, this finding is the major driving force of deep mineral exploration work in Luzong. Building 3D elaborate geological model has the important significance for prospecting to deep or surround in this area, and can help us better understand the metallogenic law and ore-controlling regularity. A 3D geological model, extending a depth from +200m to -1500m in Nihe ore deposit, has been compiled from surface geological map, cross-section, borehole logs and amounts of geological inference. And then the 3D geological models have been given physical property parameter for calculating the potential field. Modelling the potential response is proposed as means of evaluating the viability of the 3D geological models, and the evidence of making small changes to the uncertain parts of the original 3D geological models. It is expected that the final models not only reproduce supplied prior geological knowledge, but also explain the observed geophysical data. The workflow used to develop the 3D geologic model in this study includes the three major steps, as follows: (1) Determine the basic information of Model: Defining the 3D limits of the model area, the basic geological and structural unit, and the tectonic contact relations and the sedimentary sequences between these units. (2) 3D model construction: Firstly, a series of 2D geological cross sections over the model area are built by using all kinds of prior information, including surface geology, borehole data, seismic sections, and local geologists' knowledge and intuition. Lastly, we put these sections into a 3D environment according to their profile locations to build a 3D model by using geostatistics method. (3) 3D gravity and magnetic modeling: we calculate the potential field responses of the 3D model, and compare the predicted and

  16. Geodiversity: Exploration of 3D geological model space

    NASA Astrophysics Data System (ADS)

    Lindsay, M. D.; Jessell, M. W.; Ailleres, L.; Perrouty, S.; de Kemp, E.; Betts, P. G.

    2013-05-01

    The process of building a 3D model necessitates the reconciliation of field observations, geophysical interpretation, geological data uncertainty and the prevailing tectonic evolution hypotheses and interpretations. Uncertainty is compounded when clustered data points collected at local scales are statistically upscaled to one or two points for use in regional models. Interpretation is required to interpolate between sparse field data points using ambiguous geophysical data in covered terranes. It becomes clear that multiple interpretations are possible during model construction. The various interpretations are considered as potential natural representatives, but pragmatism typically dictates that just a single interpretation is offered by the modelling process. Uncertainties are introduced into the 3D model during construction from a variety of sources and through data set optimisation that produces a single model. Practices such as these are likely to result in a model that does not adequately represent the target geology. A set of geometrical ‘geodiversity’ metrics are used to analyse a 3D model of the Gippsland Basin, southeastern Australia after perturbing geological input data via uncertainty simulation. The resulting sets of perturbed geological observations are used to calculate a suite of geological 3D models that display a range of geological architectures. The concept of biodiversity has been adapted for the geosciences to quantify geometric variability, or geodiversity, between models in order to understand the effect uncertainty has models geometry. Various geometrical relationships (depth, volume, contact surface area, curvature and geological complexity) are used to describe the range of possibilities exhibited throughout the model suite. End-member models geodiversity metrics are classified in a similar manner to taxonomic descriptions. Further analysis of the model suite is performed using principal component analysis (PCA) to determine

  17. Structural interpretation of upper crust of the Khibiny area on the complex of geological and geophysical data and the results of 3D seismic and density modeling

    NASA Astrophysics Data System (ADS)

    Zhirov, Dmitry; Glaznev, Victor; Zhirova, Anzhela

    2015-04-01

    The area considered is located in the central part of the Kola Peninsula and represents a part of tectonically compound terrane, consisting of the AR, PR and PZ geological structures of the East of Fennoscandian shield (NW Russia). The Khibiny massif (PZ) intrudes the Archean complexes (the northern contact) and the Paleoproterozoic volcanogenic-sedimentary Imandra-Varzuga complex (southern and SW-contacts). Moreover this district includes several PGE-bearing layered mafic-ultramafic intrusions, which are related with Neo Archaean ÷ Paleoproterozoic rifting and plume activity (LIP). According to the previous conceptions the shape of the Khibiny multiphase pluton is close to the asymmetrical lopolit, characterized by the steep eastern and northern contacts and the gentler south and west contacts. The results of the 3D seismic and density modelling showed two correlated local high-velocity and high-density anomalies with dimensions of 5 x 10 km approximately in central part of the Khibiny massif (1) and close to contact with Imandra-Varzuga sedimentary-volcanic complex (2). The first anomaly cannot be explained by "substance" factor only (titanomagnetite-apatite ore bodies), as it has a structural disconformity to general structure of the pluton. According to the numerous instrumental measurements the actual values of stress are significantly greater than values calculated by weight of rocks. It is important the main normal axis of compressive stress has usually quasi-horizontal position. Thus, the zone of abnormally high tectonic stress is the best explanation for this anomaly. The quick isostatic uplift of the massif after the digression of the last glacier, during which the rocks did not have time to unload, can be a source of the increased horizontal stress. Based on the properties of typical rocks and geological structure of the region the second anomaly is well interpreted by large layered intrusion of Fedorova-Pana type, subsurface of which is cut by Khibiny

  18. West Flank Coso, CA FORGE 3D geologic model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

    This is an x,y,z file of the West Flank FORGE 3D geologic model. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  19. Bazhenov fm unconventional reservoir 3D geological modeling methodology

    NASA Astrophysics Data System (ADS)

    Telnova, A.; Baranov, V.; Bukhanov, N.

    2016-03-01

    The Bazhenov Formation has been studied for more than 50 years, but its petroleum potential, optimal STOIIP or resource estimation approaches, the methodology used to select a reservoir, determine its properties are still unclear. The distinctive features of bituminous shale are specific geochemical properties chosen as basic parameters to perform the geological modeling of the Bazhenov deposits and determine the key areas. The main objective of this paper is to choose an optimal 3D geological modeling algorithm and test conventional (petrophysical) and specific (geochemical) properties.

  20. Application of geologic-mathematical 3D modeling for complex structure deposits by the example of Lower- Cretaceous period depositions in Western Ust - Balykh oil field (Khanty-Mansiysk Autonomous District)

    NASA Astrophysics Data System (ADS)

    Perevertailo, T.; Nedolivko, N.; Prisyazhnyuk, O.; Dolgaya, T.

    2015-11-01

    The complex structure of the Lower-Cretaceous formation by the example of the reservoir BC101 in Western Ust - Balykh Oil Field (Khanty-Mansiysk Autonomous District) has been studied. Reservoir range relationships have been identified. 3D geologic- mathematical modeling technique considering the heterogeneity and variability of a natural reservoir structure has been suggested. To improve the deposit geological structure integrity methods of mathematical statistics were applied, which, in its turn, made it possible to obtain equal probability models with similar input data and to consider the formation conditions of reservoir rocks and cap rocks.

  1. 3D geological modeling based on gravitational and magnetic data inversion in the Luanchuan ore region, Henan Province, China

    NASA Astrophysics Data System (ADS)

    Wang, Gongwen; Zhu, Yanyan; Zhang, Shouting; Yan, Changhai; Song, Yaowu; Ma, Zhenbo; Hong, Dongming; Chen, Tianzhen

    2012-05-01

    Three-dimensional (3D) geological modeling is an important method for understanding geological structures and exploring for mineral deposits. The Luanchuan super-large molybdenum polymetallic ore region has a complex geological setting and multiple metallogenic types. 3D geological modeling is implemented by combining geological knowledge with gravitational and magnetic data inversion in the study area. The 3D geological modeling methodology and the results are summarized as follows. (1) Based on the geological setting and the deposits/occurrences, the aim was to constrain and determine the main geological objects in 3D space to construct geological and metallogenic models. (2) Based on geological observations and rock physical measurements to derive qualitative information about geological objects at depths using gravitational and magnetic data inversion, 2.5D forward modeling was used to identify shallow/subsurface geological objects, and the 3D probability method of potential field inversion was used for coarse constraining of geological objects at depths. (3) A combination of geological information with gravitational and magnetic data inversion information was used to determine the space-time genesis of metallogenic objects in potential mineral targets (i.e., Late Jurassic granite intrusions, ore-forming strata, and ore mineralization favorable faults). (4)A 3D model of the study area (17.7 km × 12.0 km × 2.5 km) is associated with the surface and subsurface geological data, which has geophysical information that is beneficial for identifying and evaluating potential prospecting zones.

  2. Coherence cube technology adds geologic insight to 3-D data

    SciTech Connect

    Morris, D.

    1997-05-01

    Three-dimensional (3-D) seismic technology is now widely applied to assess the risk associated with hydrocarbon trap definition, including faulting, stratigraphic features, and reservoir description. Critical new technologies to exploit the wealth of information contained within 3-D seismic have recently begun to emerge; most notably, coherence cube technology, developed by Amoco Production Research and licensed to Coherence Technology Co. (CTC). Coherence cube processing produces interpretable images of faults and subtle stratigraphic features, such as buried deltas, river channels, and beaches, by quantifying seismic coherence attributes. The technique has important implications for geophysical, geological, and reservoir engineering applications. The paper discusses how coherency works, applications, and an example in delineating southern North Sea faulting.

  3. Sydney-Gunnedah-Bowen Basin deep 3D structure

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

    Studies of the Sydney-Gunnedah-Bowen Basin (SGBB), one of the largest extensional rift sedimentary basins on the east coast of Australia, lack an understanding of the 3D upper crustal structure. Understanding of the subsurface structure is essential for many areas of resource exploration, development and management, as well as scientific research. Geological models provide a way to visualise and investigate the subsurface structure. The integrated regional scale gravity modelling approach, which uses boreholes and seismic data constraints, provides an understanding of the upper crustal structure and allows the development of a 3D geological model which can be used as the architectural framework for many different applications. This work presents a 3D geological model of the SGBB developed for application in high resolution thermal models. It is the culmination of geological surfaces derived from the interpolation of previous regional scale 2D gravity models and numerous borehole records. The model outlines the basement structure of the SGBB and provides information on depth to basement, depth to basal volcanics and thickness of overlying sediments. Through understanding the uncertainties, limitations, confidence and reliability of this model, the 3D geological model can provide the ideal framework for future research.

  4. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  5. From digital mapping to GIS-based 3D visualization of geological maps: example from the Western Alps geological units

    NASA Astrophysics Data System (ADS)

    Balestro, Gianni; Cassulo, Roberto; Festa, Andrea; Fioraso, Gianfranco; Nicolò, Gabriele; Perotti, Luigi

    2015-04-01

    Collection of field geological data and sharing of geological maps are nowadays greatly enhanced by using digital tools and IT (Information Technology) applications. Portable hardware allows accurate GPS localization of data and homogeneous storing of information in field databases, whereas GIS (Geographic Information Systems) applications enable generalization of field data and realization of geological map databases. A further step in the digital processing of geological map information consists of building virtual visualization by means of GIS-based 3D viewers, that allow projection and draping of significant geological features over photo-realistic terrain models. Digital fieldwork activities carried out by the Authors in the Western Alps, together with building of geological map databases and related 3D visualizations, are an example of application of the above described digital technologies. Digital geological mapping was performed by means of a GIS mobile software loaded on a rugged handheld device, and lithological, structural and geomorphological features with their attributes were stored in different layers that form the field database. The latter was then generalized through usual map processing steps such as outcrops interpolation, characterization of geological boundaries and selection of meaningful punctual observations. This map databases was used for building virtual visualizations through a GIS-based 3D-viewer that loaded detailed DTM (resolution of 5 meters) and aerial images. 3D visualizations were focused on projection and draping of significant stratigraphic contacts (e.g. contacts that separate different Quaternary deposits) and tectonic contacts (i.e. exhumation-related contacts that dismembered original ophiolite sequences). In our experience digital geological mapping and related databases ensured homogeneous data storing and effective sharing of information, and allowed subsequent building of 3D GIS-based visualizations. The latters gave

  6. The capture and dissemination of integrated 3D geospatial knowledge at the British Geological Survey using GSI3D software and methodology

    NASA Astrophysics Data System (ADS)

    Kessler, Holger; Mathers, Steve; Sobisch, Hans-Georg

    2009-06-01

    The Geological Surveying and Investigation in 3 Dimensions (GSI3D) software tool and methodology has been developed over the last 15 years. Since 2001 this has been in cooperation with the British Geological Survey (BGS). To-date over a hundred BGS geologists have learned to use the software that is now routinely deployed in building systematic and commercial 3D geological models. The success of the GSI3D methodology and software is based on its intuitive design and the fact that it utilises exactly the same data and methods, albeit in digital forms, that geologists have been using for two centuries in order to make geological maps and cross-sections. The geologist constructs models based on a career of observation of geological phenomena, thereby incorporating tacit knowledge into the model. This knowledge capture is a key element to the GSI3D approach. In BGS GSI3D is part of a much wider set of systems and work processes that together make up the cyberinfrastructure of a modern geological survey. The GSI3D software is not yet designed to cope with bedrock structures in which individual stratigraphic surfaces are repeated or inverted, but the software is currently being extended by BGS to encompass these more complex geological scenarios. A further challenge for BGS is to enable its 3D geological models to become part of the semantic Web using GML application schema like GeoSciML. The biggest benefits of widely available systematic geological models will be an enhanced public understanding of the sub-surface in 3D, and the teaching of geoscience students.

  7. Structural Geology

    NASA Astrophysics Data System (ADS)

    Weber, John; Frankel, Kurt L.

    2011-05-01

    Structural geology and continental tectonics were ushered in to the modern quantitative age of geosciences with the arrival of the global plate tectonics paradigm (circa 1968), derived using new data from the oceans' depths, and John Ramsay's 1967 seminal work, Folding and Fracturing of Rocks. Fossen is to be applauded for crafting a unique, high-caliber, and accessible undergraduate textbook on structural geology that faithfully reflects this advance and the subsequent evolution of the discipline. This well-written text draws on Fossen's wealth of professional experience, including his broad and diverse academic research and experience in the petroleum industry. This book is beautifully illustrated, with excellent original color diagrams and with impressive color field photographs that are all keyed to locations and placed into geologic context.

  8. 3D imaging of geological structures by R-VSP utilizing vibrations caused by shaft excavations at the Mizunami Underground Research Laboratory in Japan

    NASA Astrophysics Data System (ADS)

    Matsuoka, T.; Hodotsuka, Y.; Ishigaki, K.; Lee, C.

    2009-12-01

    Japan Atomic Energy Agency is now conducting the Mizunami Underground Research Laboratory (MIU) project. The MIU consists of two shafts (main shaft: 6.5m, ventilation shaft: 4.5m diameter) and horizontal research galleries, in sedimentary and granitic rocks at Mizunami City, Central Japan. The MIU project is a broad scientific study of the deep geological environment providing the basis for research and development for geological disposal of high level radioactive waste. One of the main goals is to establish techniques for investigation, analysis and assessment of the deep geological environment in fractured crystalline rock. As a part of the MIU project, we carried out the Reverse-Vertical Seismic Profile (R-VSP) using vibrations from the blasting for the shaft excavations and drilling of boreholes in the horizontal research galleries and examined the applicability of this method to imaging of geological structures around underground facilities, such as the unconformity between the sedimentary rocks and the basal granite, and faults and fracture zones in the granite. R-VSP method is a seismic method utilizing the receiver arrays on surface and seismic sources underground (e.g. in boreholes). This method is advantageous in that planning of 3-dimensional surveys is easy compared with reflection seismic surveying and conventional VSP because seismic source arrays that are major constraint for conducting surveys on surface are unnecessary. The receiver arrays consist of six radial lines on surface with a central focus on the main shaft. Seven blast rounds for the main shaft excavation from GL-52.8m to GL-250m and the borehole drilling in the GL-200m horizontal research gallery were observed. Three types of data processing, conventional VSP data processing (VSP-CDP transform and VSP migration), Reflection data processing utilizing Seismic interferometry method (“Seismic interferometry”) and Reflection mapping utilizing Image Point transform method (“IP transform

  9. Structured light field 3D imaging.

    PubMed

    Cai, Zewei; Liu, Xiaoli; Peng, Xiang; Yin, Yongkai; Li, Ameng; Wu, Jiachen; Gao, Bruce Z

    2016-09-01

    In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces. PMID:27607639

  10. 3D reconstruction of complex geological bodies: Examples from the Alps

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Francesca, Salvi; Stefano, Zanchetta; Simone, Sterlacchini; Graziano, Guerra

    2009-01-01

    Cartographic geological and structural data collected in the field and managed by Geographic Information Systems (GIS) technology can be used for 3D reconstruction of complex geological bodies. Using a link between GIS tools and gOcad, stratigraphic and tectonic surfaces can be reconstructed taking into account any geometrical constraint derived from field observations. Complex surfaces can be reconstructed using large data sets analysed by suitable geometrical techniques. Three main typologies of geometric features and related attributes are exported from a GIS-geodatabase: (1) topographic data as points from a digital elevation model; (2) stratigraphic and tectonic boundaries, and linear features as 2D polylines; (3) structural data as points. After having imported the available information into gOcad, the following steps should be performed: (1) construction of the topographic surface by interpolation of points; (2) 3D mapping of the linear geological boundaries and linear features by vertical projection on the reconstructed topographic surface; (3) definition of geometrical constraints from planar and linear outcrop data; (4) construction of a network of cross-sections based on field observations and geometrical constraints; (5) creation of 3D surfaces, closed volumes and grids from the constructed objects. Three examples of the reconstruction of complex geological bodies from the Italian Alps are presented here. The methodology demonstrates that although only outcrop data were available, 3D modelling has allows the checking of the geometrical consistency of the interpretative 2D sections and of the field geology, through a 3D visualisation of geometrical models. Application of a 3D geometrical model to the case studies can be very useful in geomechanical modelling for slope-stability or resource evaluation.

  11. Delivery mechanisms of 3D geological models - a perspective from the British Geological Survey

    NASA Astrophysics Data System (ADS)

    Terrington, Ricky; Myers, Antony; Wood, Ben; Arora, Baneet

    2013-04-01

    The past decade has seen the British Geological Survey (BGS) construct over one hundred 3D geological models using software such as GOCAD®, GSI3D, EarthVision and Petrel across the United Kingdom and overseas. These models have been produced for different purposes and at different scales and resolutions in the shallow and deep subsurface. Alongside the construction of these models, the BGS and its collaborators have developed several options for disseminating these 3D geological models to external partners and the public. Initially, the standard formats for disseminating these 3D geological models by the BGS comprised of 2D images of cross-sections, GIS raster data and specialised visualisation software such as the LithoFrame Viewer. The LithoFrame Viewer is a thick-client software that allows the user to explore the 3D geometries of the geological units using a 3D interface, and generate synthetic cross-sections and boreholes on the fly. Despite the increased functionality of the LithoFrame Viewer over the other formats, the most popular data formats distributed remained 2D images of cross-sections, CAD based formats (e.g. DWG and DXF) and GIS raster data of surfaces and thicknesses, as these were the types of data that the external partners were most used too. Since 2009 software for delivering 3D geological models has advanced and types of data available have increased. Feature Manipulation Engine (FME) has been used to increase the number of outputs from 3D geological models. These include: • 3D PDFs (Adobe Acrobat) • KMZ/KML (GoogleEarth) • 3D shapefiles (ESRI) Alongside these later outputs, the BGS has developed other software such as GroundhogTM and Geovisionary (in collaboration with Virtalis). Groundhog is fully a web based application that allows the user to generate synthetic cross-sections, boreholes and horizontal slices from 3D geological models on the fly. Geovisionary provides some of the most advanced visualisation of 3D geological models in

  12. Improving hydrogeological models of deltaic sedimentary media using GIS based 3D geological tools

    NASA Astrophysics Data System (ADS)

    Velasco, V.; Gogu, R.; Vázquez-Suñé, E.; Monfort, D.; Garriga, A.; Carrera, J.

    2009-04-01

    Due to the natural heterogeneity the hydrological modeling in the deltaic sedimentary media is complex. Reliable 3D hydrogeological models could be created by integrating properly detailed and accurate data. This data has to be properly managed and interpreted. The first task has been the creation of a geospatial database to store and to allow the management of a great amount of different data types coming from different sources (geophysical, geological, hydraulic, and others). The data structure allows storing an accurate and very detailed core geological description that can be straightforwardly generalized and further upscaled. The second step was to create tools within a GIS environment allowing querying and visualizing the data. One consists in illustrating the core with the detailed geological description of each selected borehole. Another creates geologic profiles by using an on screen defined buffer zone selection for the needed boreholes. The lithological columns of the boreholes together with the defined stratigraphic subunits appear on screen as a geological profile. Complementary information like the DTM profile, the distance between the boreholes, the depth of each strata complete the geological picture. In this working environment the user is able to analyze the possible existing stratigraphical units and to define them on screen in a deterministic way or by using geostatistics. Additionally information like the type of the contact surface, the position between the geological units or subunits as well as other parameters could be attached as attributes. The possible faults or fractures can be identified within the same environment. To date, a dictionary of terms describing the possible geological contact surfaces types is on the way to be defined. In parallel, a tool of converting the geological units/subunits analyzed data is developed in order to project the obtained information within a 3D environment. The export procedure provides a spatial

  13. Genetic approach to reconstruct complex regional geological setting of the Baltic basin in 3D geological model

    NASA Astrophysics Data System (ADS)

    Popovs, K.; Saks, T.; Ukass, J.; Jatnieks, J.

    2012-04-01

    Interpretation of geological structures in 3D geological models is a relatively new research topic that is already standardized in many geological branches. Due to its wide practical application, these models are indispensable and become one of the dominant interpretation methods in reducing geological uncertainties in many geology fields. Traditionally, geological concepts complement quantitative as much as qualitative data to obtain a model deemed acceptable, however, available data very often is insufficient and modeling methods primarily focus on spatial data but geological history usually is mostly neglected for the modeling of large sedimentary basins. A need to better integrate the long and often complex geological history and geological knowledge into modeling procedure is very acute to gain geological insight and improve the quality of geological models. During this research, 3D geological model of the Baltic basin (BB) was created. Because of its complex regional geological setting - wide range of the data sources with multiple scales, resolution and density as well as its various source formats, the study area provides a challenge for the 3D geological modeling. In order to create 3D regional geometrical model for the study area algorithmic genetic approach for model geometry reconstruction was applied. The genetic approach is based on the assumption that post-depositional deformation produce no significant change in sedimentary strata volume, assuming that the strata thickness and its length in a cross sectional plane remains unchanged except as a result of erosion. Assuming that the tectonic deformation occurred in sequential cycles and subsequent tectonic stage strata is separated by regional unconformity as is the case of the BB, there is an opportunity for algorithmic approach in reconstructing these conditions by sequentially reconstructing the layer original thickness. Layer thicknesses were sliced along fault lines, where applicable layer

  14. Building 3D geological knowledge through regional scale gravity modelling for the Bowen Basin

    NASA Astrophysics Data System (ADS)

    Danis, Cara; O'Neill, Craig; Lackie, Mark

    2012-01-01

    Regional scale gravity modelling is an effective and fast way to gain geological understanding of large scale structures like the Bowen Basin. Detailed deep 3D geological knowledge has become an important component of many types of exploration and resource modelling. Current interest in the Bowen Basin for geothermal exploration highlights the need for a complete basin scale model which is compatible with thermal modelling software. The structure of the Bowen Basin is characteristic of a typical asymmetrical extensional rift basin, with up to 5km of sediment overlying the basement. By combining gravity modelling, calibrated by boreholes and seismic reflection profiles, we produce geologically reasonable 3D surfaces and structures to create a model of the Bowen Basin. This model is the final part in the completion of the 3D Sydney-Gunnedah-Bowen Basin system geological model and provides both an important framework from which detailed thermal models can be derived and a platform from which to expand with new information.

  15. How to find what you don't know: Visualising variability in 3D geological models

    NASA Astrophysics Data System (ADS)

    Lindsay, Mark; Wellmann, Florian; Jessell, Mark; Ailleres, Laurent

    2014-05-01

    Uncertainties in input data can have compounding effects on the predictive reliability of three-dimensional (3D) geological models. Resource exploration, tectonic studies and environmental modelling can be compromised by using 3D models that misrepresent the target geology, and drilling campaigns that attempt to intersect particular geological units guided by 3D models are at risk of failure if the exploration geologist is unaware of inherent uncertainties. In addition, the visual inspection of 3D models is often the first contact decision makers have with the geology, thus visually communicating the presence and magnitude of uncertainties contained within geological 3D models is critical. Unless uncertainties are presented early in the relationship between decision maker and model, the model will be considered more truthful than the uncertainties allow with each subsequent viewing. We present a selection of visualisation techniques that provide the viewer with an insight to the location and amount of uncertainty contained within a model, and the geological characteristics which are most affected. A model of the Gippsland Basin, southeastern Australia is used as a case study to demonstrate the concepts of information entropy, stratigraphic variability and geodiversity. Central to the techniques shown here is the creation of a model suite, performed by creating similar (but not the same) version of the original model through perturbation of the input data. Specifically, structural data in the form of strike and dip measurements is perturbed in the creation of the model suite. The visualisation techniques presented are: (i) information entropy; (ii) stratigraphic variability and (iii) geodiversity. Information entropy is used to analyse uncertainty in a spatial context, combining the empirical probability distributions of multiple outcomes with a single quantitative measure. Stratigraphic variability displays the number of possible lithologies that may exist at a

  16. 3D geological model developed to analyse the aquifer - sewer network interaction in Bucharest city

    NASA Astrophysics Data System (ADS)

    Serpescu, I.; Radu, E.; Gogu, R. G.; Priceputu, A.; Boukhemacha, M. A.; Bica, I.; Gaitanaru, D.

    2012-04-01

    their thickness. Further structural maps have been generated to outline the spatial development of the existing aquifers. By connecting the 3D sewer network to the geology, a qualitative description of the interaction between the aquifer media and the sewer system is obtained as a 3D geometrical model.

  17. Will true 3d display devices aid geologic interpretation. [Mirage

    SciTech Connect

    Nelson, H.R. Jr.

    1982-04-01

    A description is given of true 3D display devices and techniques that are being evaluated in various research laboratories around the world. These advances are closely tied to the expected application of 3D display devices as interpretational tools for explorationists. 34 refs.

  18. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen. PMID:25690896

  19. Canada in 3D - Toward a Sustainable 3D Model for Canadian Geology from Diverse Data Sources

    NASA Astrophysics Data System (ADS)

    Brodaric, B.; Pilkington, M.; Snyder, D. B.; St-Onge, M. R.; Russell, H.

    2015-12-01

    Many big science issues span large areas and require data from multiple heterogeneous sources, for example climate change, resource management, and hazard mitigation. Solutions to these issues can significantly benefit from access to a consistent and integrated geological model that would serve as a framework. However, such a model is absent for most large countries including Canada, due to the size of the landmass and the fragmentation of the source data into institutional and disciplinary silos. To overcome these barriers, the "Canada in 3D" (C3D) pilot project was recently launched by the Geological Survey of Canada. C3D is designed to be evergreen, multi-resolution, and inter-disciplinary: (a) it is to be updated regularly upon acquisition of new data; (b) portions vary in resolution and will initially consist of four layers (surficial, sedimentary, crystalline, and mantle) with intermediary patches of higher-resolution fill; and (c) a variety of independently managed data sources are providing inputs, such as geophysical, 3D and 2D geological models, drill logs, and others. Notably, scalability concerns dictate a decentralized and interoperable approach, such that only key control objects, denoting anchors for the modeling process, are imported into the C3D database while retaining provenance links to original sources. The resultant model is managed in the database, contains full modeling provenance as well as links to detailed information on rock units, and is to be visualized in desktop and online environments. It is anticipated that C3D will become the authoritative state of knowledge for the geology of Canada at a national scale.

  20. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

    Recent experimental and theoretical ideas are laying the ground for a new era in the knowledge of the parton structure of nuclei. We report on two promising directions beyond inclusive deep inelastic scattering experiments, aimed at, among other goals, unveiling the three-dimensional structure of the bound nucleon. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative content is parametrized in terms of generalized parton distributions. In this way the distribution of partons in the transverse plane will be obtained, providing a pictorial view of the realization of the European Muon Collaboration effect. In particular, we show how, through the generalized parton distribution framework, non-nucleonic degrees of freedom in nuclei can be unveiled. Analogously, the momentum space 3D structure can be accessed by studying transverse-momentum-dependent parton distributions in semi-inclusive deep inelastic scattering processes. The status of measurements is also summarized, in particular novel coincidence measurements at high-luminosity facilities, such as Jefferson Laboratory. Finally the prospects for the next years at future facilities, such as the 12GeV Jefferson Laboratory and the Electron Ion Collider, are presented.

  1. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

    Siler, Drew L; Faulds, James E; Mayhew, Brett; McNamara, David

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

  2. Hands-on guide for 3D image creation for geological purposes

    NASA Astrophysics Data System (ADS)

    Frehner, Marcel; Tisato, Nicola

    2013-04-01

    Geological structures in outcrops or hand specimens are inherently three dimensional (3D), and therefore better understandable if viewed in 3D. While 3D models can easily be created, manipulated, and looked at from all sides on the computer screen (e.g., using photogrammetry or laser scanning data), 3D visualizations for publications or conference posters are much more challenging as they have to live in a 2D-world (i.e., on a sheet of paper). Perspective 2D visualizations of 3D models do not fully transmit the "feeling and depth of the third dimension" to the audience; but this feeling is desirable for a better examination and understanding in 3D of the structure under consideration. One of the very few possibilities to generate real 3D images, which work on a 2D display, is by using so-called stereoscopic images. Stereoscopic images are two images of the same object recorded from two slightly offset viewpoints. Special glasses and techniques have to be used to make sure that one image is seen only by one eye, and the other image is seen by the other eye, which together lead to the "3D effect". Geoscientists are often familiar with such 3D images. For example, geomorphologists traditionally view stereographic orthophotos by employing a mirror-steroscope. Nowadays, petroleum-geoscientists examine high-resolution 3D seismic data sets in special 3D visualization rooms. One of the methods for generating and viewing a stereoscopic image, which does not require a high-tech viewing device, is to create a so-called anaglyph. The principle is to overlay two images saturated in red and cyan, respectively. The two images are then viewed through red-cyan-stereoscopic glasses. This method is simple and cost-effective, but has some drawbacks in preserving colors accurately. A similar method is used in 3D movies, where polarized light or shuttering techniques are used to separate the left from the right image, which allows preserving the original colors. The advantage of red

  3. Parameterization of training images for aquifer 3-D facies modeling integrating geological interpretations and statistical inference

    NASA Astrophysics Data System (ADS)

    Jha, Sanjeev Kumar; Comunian, Alessandro; Mariethoz, Gregoire; Kelly, Bryce F. J.

    2014-10-01

    We develop a stochastic approach to construct channelized 3-D geological models constrained to borehole measurements as well as geological interpretation. The methodology is based on simple 2-D geologist-provided sketches of fluvial depositional elements, which are extruded in the 3rd dimension. Multiple-point geostatistics (MPS) is used to impair horizontal variability to the structures by introducing geometrical transformation parameters. The sketches provided by the geologist are used as elementary training images, whose statistical information is expanded through randomized transformations. We demonstrate the applicability of the approach by applying it to modeling a fluvial valley filling sequence in the Maules Creek catchment, Australia. The facies models are constrained to borehole logs, spatial information borrowed from an analogue and local orientations derived from the present-day stream networks. The connectivity in the 3-D facies models is evaluated using statistical measures and transport simulations. Comparison with a statistically equivalent variogram-based model shows that our approach is more suited for building 3-D facies models that contain structures specific to the channelized environment and which have a significant influence on the transport processes.

  4. Discovering Structural Regularity in 3D Geometry

    PubMed Central

    Pauly, Mark; Mitra, Niloy J.; Wallner, Johannes; Pottmann, Helmut; Guibas, Leonidas J.

    2010-01-01

    We introduce a computational framework for discovering regular or repeated geometric structures in 3D shapes. We describe and classify possible regular structures and present an effective algorithm for detecting such repeated geometric patterns in point- or mesh-based models. Our method assumes no prior knowledge of the geometry or spatial location of the individual elements that define the pattern. Structure discovery is made possible by a careful analysis of pairwise similarity transformations that reveals prominent lattice structures in a suitable model of transformation space. We introduce an optimization method for detecting such uniform grids specifically designed to deal with outliers and missing elements. This yields a robust algorithm that successfully discovers complex regular structures amidst clutter, noise, and missing geometry. The accuracy of the extracted generating transformations is further improved using a novel simultaneous registration method in the spatial domain. We demonstrate the effectiveness of our algorithm on a variety of examples and show applications to compression, model repair, and geometry synthesis. PMID:21170292

  5. Sheet 280—Fossombrone 3D: A study project for a new geological map of Italy in three dimensions

    NASA Astrophysics Data System (ADS)

    De Donatis, Mauro; Borraccini, Francesco; Susini, Sara

    2009-01-01

    The goal of this project is to define and test a method for building a three-dimensional (3D) geological model of Italy based on maps at a 1:50,000 scale, using the new national geological mapping program (CARG project). A structural model of Sheet 280—Fossombrone (Northern Apennines, central Italy) was produced using recently developed 3D visualization techniques. This area is characterized by faulted anticlines and broad synclines, involving a Triassic-Palaeogene succession detached from its underlying basement. Exhaustive knowledge of the regional and local geology, combined with available subsurface (well and seismic) data, makes this area a good test site for developing a 3D geological modeling method. The model of Sheet 280—Fossombrone was built in two steps. In the first step, we built a 2.5D geological model using the digital elevation model combined with the new 1:50,000 scale geological map of the area. This 2.5D model shows relationships between topographic elements, geology and major structures much better than traditional 2D geological maps. In the second step, we constructed an in-depth model integrating a large amount of subsurface data with field data from the recent mapping project. The geological model of Sheet 280—Fossombrone clarifies structural geometries and kinematics of this external part of the Northern Apennines. Structural and geomorphic analyses were performed on the 3D model to evaluate how additional information can be obtained from 3D cartography in order to improve knowledge of the study area. We present results of these analyses as examples.

  6. 3D Strucutural Geological Model of the Alpi Mt. Area (Southern Italy)

    NASA Astrophysics Data System (ADS)

    La Bruna, Vincenzo; Lamarche, Juliette; Viseur, Sophie; Agosta, Fabrizio; Prosser, Giacomo

    2016-04-01

    The study area is located in the inner portion of the southern Apennines fold-and-thrust belt. The Alpi Mt. is the only portion of the Apulian domain cropping in this sector. In fact, it is considered as a structural analogue of the Val d'Agri and Tempa Rossa reservoirs (Basilicata). The Alpi Mt. tectonic unit is composed of two main cronostratigraphic intervals, represented by a 2000m-thick Mesozoic carbonate succession and a Messinian mixed carbonate-terrigenous succession. The Messinian interval is made up of a Lower Messinian sedimentary cycle, wich form a paraconformity with the underlying Mesozoic carbonates, and an Upper Messinian cycle characterized by a marked unconformity at the bottom. This study aims to better understand the role exerted by the precontractional tectonic structures during the Messinian interval, wich are responsible for the development of the sedimentary angular unconformity. To reach this goal, a 3D structural geological model was build up by using the Gocad(R) software. The construction of the 3D model was gained through the integration of several results related to geological field mapping, well log analysis and seismic reflection data. Focusing on the Upper Messinian sedimentary horizon, in order to achieve the true geometry and kinematics of the high-angle extensional faults that bound the sedimentary depocenters, the model was restored through vertical line methodology. This process allows to obtain more information about location, geometry, and sedimentary depocenter orientations. Furthermore, the 3D structural model brings some important results from the 3D fault analysis that are represented by attitude, geometry and dimensional parameters of the fault network that affect the study area.

  7. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    PubMed

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  8. Numerical homogenization for seismic wave propagation in 3D geological media

    NASA Astrophysics Data System (ADS)

    Cupillard, P.; Capdeville, Y.; Botella, A.

    2014-12-01

    Despite the important increase of the computational power in the last decades, simulating the seismic wave propagation through realistic geological models is still a challenge. By realistic models we here mean 3D media in which a broad variety (in terms of amplitude and extent) of heterogeneities lies, including discontinuities with complex geometry such as faulted and folded horizons, intrusive geological contacts and fault systems. To perform accurate numerical simulations, these discontinuities require complicated meshes which usually contain extremely small elements, yielding large, sometimes prohibitive, computation costs. Fortunately, the recent development of the non-periodic homogenization technique now enables to overcome this problem by computing smooth equivalent models for which a coarse mesh is sufficient to get an accurate wavefield. In this work, we present an efficient implementation of the technique which now allows for the homogenization of large 3D geological models. This implementation relies on a tetrahedral finite-element solution of the elasto-static equation behind the homogenization problem. Because this equation is time-independent, solving it is numerically cheaper than solving the wave equation, but it nevertheless requires some care because of the large size of the stiffness matrix arising from the fine mesh of realistic geological structures. A domain decomposition is therefore adopted. In our strategy, the obtained sub-domains overlap but they are independent so the solution within each of them can be computed either in series or in parallel. In addition, well-balanced loads, efficient search algorithms and multithreading are implemented to speed up the computation. The resulting code enables the homogenization of 3D elastic media in a time that is neglectable with respect to the simulation time of the wave propagation within. This is illustrated through a sub-surface model of the Furfooz karstic region, Belgium.

  9. Discovery of previously unrecognised local faults in London, UK, using detailed 3D geological modelling

    NASA Astrophysics Data System (ADS)

    Aldiss, Don; Haslam, Richard

    2013-04-01

    In parts of London, faulting introduces lateral heterogeneity to the local ground conditions, especially where construction works intercept the Palaeogene Lambeth Group. This brings difficulties to the compilation of a ground model that is fully consistent with the ground investigation data, and so to the design and construction of engineering works. However, because bedrock in the London area is rather uniform at outcrop, and is widely covered by Quaternary deposits, few faults are shown on the geological maps of the area. This paper discusses a successful resolution of this problem at a site in east central London, where tunnels for a new underground railway station are planned. A 3D geological model was used to provide an understanding of the local geological structure, in faulted Lambeth Group strata, that had not been possible by other commonly-used methods. This model includes seven previously unrecognised faults, with downthrows ranging from about 1 m to about 12 m. The model was constructed in the GSI3D geological modelling software using about 145 borehole records, including many legacy records, in an area of 850 m by 500 m. The basis of a GSI3D 3D geological model is a network of 2D cross-sections drawn by a geologist, generally connecting borehole positions (where the borehole records define the level of the geological units that are present), and outcrop and subcrop lines for those units (where shown by a geological map). When the lines tracing the base of each geological unit within the intersecting cross-sections are complete and mutually consistent, the software is used to generate TIN surfaces between those lines, so creating a 3D geological model. Even where a geological model is constructed as if no faults were present, changes in apparent dip between two data points within a single cross-section can indicate that a fault is present in that segment of the cross-section. If displacements of similar size with the same polarity are found in a series

  10. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

    González-Torre, Iván; Losada, Juan Carlos; Falconer, Ruth; Hapca, Simona; Tarquis, Ana M.

    2015-04-01

    Soil structure may be defined as the spatial arrangement of soil particles, aggregates and pores. The geometry of each one of these elements, as well as their spatial arrangement, has a great influence on the transport of fluids and solutes through the soil. Fractal/Multifractal methods have been increasingly applied to quantify soil structure thanks to the advances in computer technology (Tarquis et al., 2003). There is no doubt that computed tomography (CT) has provided an alternative for observing intact soil structure. These CT techniques reduce the physical impact to sampling, providing three-dimensional (3D) information and allowing rapid scanning to study sample dynamics in near real-time (Houston et al., 2013a). However, several authors have dedicated attention to the appropriate pore-solid CT threshold (Elliot and Heck, 2007; Houston et al., 2013b) and the better method to estimate the multifractal parameters (Grau et al., 2006; Tarquis et al., 2009). The aim of the present study is to evaluate the effect of the algorithm applied in the multifractal method (box counting and box gliding) and the cube size on the calculation of generalized fractal dimensions (Dq) in grey images without applying any threshold. To this end, soil samples were extracted from different areas plowed with three tools (moldboard, chissel and plow). Soil samples for each of the tillage treatment were packed into polypropylene cylinders of 8 cm diameter and 10 cm high. These were imaged using an mSIMCT at 155keV and 25 mA. An aluminium filter (0.25 mm) was applied to reduce beam hardening and later several corrections where applied during reconstruction. References Elliot, T.R. and Heck, R.J. 2007. A comparison of 2D and 3D thresholding of CT imagery. Can. J. Soil Sci., 87(4), 405-412. Grau, J, Médez, V.; Tarquis, A.M., Saa, A. and Díaz, M.C.. 2006. Comparison of gliding box and box-counting methods in soil image analysis. Geoderma, 134, 349-359. González-Torres, Iván. Theory and

  11. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

    PubMed Central

    Sarver, Michael; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B.

    2010-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, “Find RNA 3D” (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs

  12. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

    Recent advances in the 3-D reconstruction of planetary nebulae are reviewed. We include not only results for 3-D reconstructions, but also the current techniques in terms of general methods and software. In order to obtain more accurate reconstructions, we suggest to extend the widely used assumption of homologous nebula expansion to map spectroscopically measured velocity to position along the line of sight.

  13. Integration of geostatistical techniques and intuitive geology in the 3-D modeling process

    SciTech Connect

    Heine, C.J.; Cooper, D.H.

    1995-08-01

    The development of 3-D geologic models for reservoir description and simulation has traditionally relied on the computer derived interpolation of well data in a geocelluar stratigraphic framework. The quality of the interpolation has been directly dependent on the nature of the interpolation method, and ability of the interpolation scheme to accurately predict the value of geologic attributes away from the well. Typically, interpolation methods employ deterministic or geostatistical algorithms which offer limited capacity for integrating data derived from secondary analyses. These secondary analyses, which might include the results from 3-D seismic inversion, borehole imagery studies, or deductive reasoning, introduce a subjective component into what would otherwise be restricted to a purely mathematical treatment of geologic data. At Saudi ARAMCO an increased emphasis is being placed on the role of the reservoir geologist in the development of 3-D geologic models. Quantitative results, based on numerical computations, are being enhanced with intuitive geology, derived from years of cumulative professional experience and expertise. Techniques such as template modeling and modified conditional simulation, are yielding 3-D geologic models, which not only more accurately reflect the geology of the reservoir, but also preserve geologic detail throughout the simulation process. This incorporation of secondary data sources and qualitative analysis has been successfully demonstrated in a clastic reservoir environment in Central Saudi Arabia, and serves as a prototype for future 3-D geologic model development.

  14. Integration of geostatistical techniques and intuitive geology in the 3-D modeling process

    SciTech Connect

    Heine, C.J.; Cooper, D.H. )

    1996-01-01

    The development of 3-D geologic models for reservoir description and simulation has traditionally relied on the computer derived interpolation of well data in a geocelluar stratigraphic framework. The quality of the interpolation has been directly dependent on the nature of the interpolation method, and ability of the Interpolation scheme to accurately predict the value of geologic attributes away from the well. Typically, interpolation methods employ deterministic or geostatistical algorithms which offer limited capacity for Integrating data derived from secondary analyses. These secondary analyses, which might include the results from 3-D seismic inversion, borehole imagery studies, or deductive reasoning, introduce a subjective component into what would otherwise be restricted to a purely mathematical treatment of geologic data. At Saudi ARAMCO an increased emphases is being placed on the role of the reservoir geologist in the development of 3-D geologic models. Quantitative results, based on numerical computations, are being enhanced with intuitive geology, derived from years of cumulative professional experience and expertise. Techniques such as template modeling and modified conditional simulation, are yielding 3-D geologic models, which not only more accurately reflect the geology of the reservoir, but also preserve geologic detail throughout the simulation process. This incorporation of secondary data sources and qualitative analysis has been successfully demonstrated in a clastic reservoir environment in Central Saudi Arabia, and serves as a prototype for future 3-D geologic model development.

  15. Integration of geostatistical techniques and intuitive geology in the 3-D modeling process

    SciTech Connect

    Heine, C.J.; Cooper, D.H.

    1996-12-31

    The development of 3-D geologic models for reservoir description and simulation has traditionally relied on the computer derived interpolation of well data in a geocelluar stratigraphic framework. The quality of the interpolation has been directly dependent on the nature of the interpolation method, and ability of the Interpolation scheme to accurately predict the value of geologic attributes away from the well. Typically, interpolation methods employ deterministic or geostatistical algorithms which offer limited capacity for Integrating data derived from secondary analyses. These secondary analyses, which might include the results from 3-D seismic inversion, borehole imagery studies, or deductive reasoning, introduce a subjective component into what would otherwise be restricted to a purely mathematical treatment of geologic data. At Saudi ARAMCO an increased emphases is being placed on the role of the reservoir geologist in the development of 3-D geologic models. Quantitative results, based on numerical computations, are being enhanced with intuitive geology, derived from years of cumulative professional experience and expertise. Techniques such as template modeling and modified conditional simulation, are yielding 3-D geologic models, which not only more accurately reflect the geology of the reservoir, but also preserve geologic detail throughout the simulation process. This incorporation of secondary data sources and qualitative analysis has been successfully demonstrated in a clastic reservoir environment in Central Saudi Arabia, and serves as a prototype for future 3-D geologic model development.

  16. STAR3D: a stack-based RNA 3D structural alignment tool

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  17. STAR3D: a stack-based RNA 3D structural alignment tool.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  18. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    PubMed

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

    2015-07-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  19. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    PubMed Central

    Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  20. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  1. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  2. Norg underground gas storage - an integrated 3-D geological and geophysical reservoir modeling study

    SciTech Connect

    Cohen, J.; Smith, S. ); Huis, R.; Copper, J.; Whyte, S. )

    1993-09-01

    The Netherlands have an extensive gas distribution infrastructure supplying 80 x 10[sup 9] m[sup 3] per annum to the domestic and European market. The capacity requirement exceeds 600 x 10[sup 6] sm[sup 3]/d, of which 430 x 10[sup 6] sm[sup 3]/d is provided by the giant Groningen gas field. The Groningen field will soon reach a pressure at which this capacity can no longer be met without considerable investments. It will also become difficult to maintain the market gas quality, because of the increasing supply from small fields with widely varying gas qualities. Underground Gas Storage (UGS) will satisfy both capacity and gas-quality requirements. This UGS must eventually store 4.5 x 10[sup 9] m[sup 3] with injection/production capacities of 36/80-100 x 10[sup 6] sm[sup 3]/d, making it one of the largest UGS projects in the world. These extremely high-capacity requirements demand both high-matrix permeability and good understanding of vertical and lateral reservoir continuity. Matrix permeability is predictable due to the close relationship with the lithofacies defined within the primary Rotliegende depositional model. Minor faults, identified on three-dimensional (3-D) seismic attribute maps, represent potential transmissibility impairment zones, compartmentalizing the reservoir. This was initially suggested by core fracture studies and confirmed by a subsequent field shut-in and pressure buildup test. Lithofacies and seismic structural data are integrated within a computerized reservoir geological modeling system known as [open quotes]Monarch[close quotes] to provide a highly detailed 3-D permeability model that is then tranformed into a model for dynamic reservoir simulation. The results confirm the required working volume for the UGS operation and provide a basis for the initial field development planning.

  3. Using 3D Geologic Models to Synthesize Large and Disparate Datasets for Site Characterization and Verification Purposes

    NASA Astrophysics Data System (ADS)

    Hillesheim, M. B.; Rautman, C. A.; Johnson, P. B.; Powers, D. W.

    2008-12-01

    As we are all aware, increases in computing power and efficiency have allowed for the development of many modeling codes capable of processing large and sometimes disparate datasets (e.g., geological, hydrological, geochemical, etc). Because people sometimes have difficulty visualizing in three dimensions (3D) or understanding how multiple figures of various geologic features relate as a whole, 3D geologic models can be excellent tools to illustrate key concepts and findings, especially to lay persons, such as stakeholders, customers, and other concerned parties. In this presentation, we will show examples of 3D geologic modeling efforts using data collected during site characterization and verification work at the Waste Isolation Pilot Plant (WIPP). The WIPP is a U.S. Department of Energy (DOE) facility located in southeastern New Mexico, designed for the safe disposal of transuranic wastes resulting from U.S. defense programs. The 3D geologic modeling efforts focused on refining our understanding of the WIPP site by integrating a variety of geologic data. Examples include: overlaying isopach surfaces of unit thickness and overburden thickness, a map of geologic facies changes, and a transmissivity field onto a 3D structural map of a geologic unit of interest. In addition, we also present a 4D hydrogeologic model of the effects of a large-scale pumping test on water levels. All these efforts have provided additional insights into the controls on transmissivity and flow in the WIPP vicinity. Ultimately, by combining these various types of data we have increased our understanding of the WIPP site's hydrogeologic system, which is a key aspect of continued certification. Sandia is a multi program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04- 94AL85000. This research is funded by WIPP programs administered by the Office of Environmental

  4. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

  5. Impacts of a CAREER Award on Advancing 3D Visualization in Geology Education

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2011-12-01

    CAREER awards provide a unique opportunity to develop educational activities as an integrated part of one's research activities. This CAREER award focused on developing interactive 3D visualization tools to aid geology students in improving their 3D visualization skills. Not only is this a key skill for field geologists who need to visualize unseen subsurface structures, but it is also an important aspect of geodynamic research into the processes, such as faulting and viscous flow, that occur during subduction. Working with an undergraduate student researcher and using the KeckCAVES developed volume visualization code 3DVisualizer, we have developed interactive visualization laboratory exercises (e.g., Discovering the Rule of Vs) and a suite of mini-exercises using illustrative 3D geologic structures (e.g., syncline, thrust fault) that students can explore (e.g., rotate, slice, cut-away) to understand how exposure of these structures at the surface can provide insight into the subsurface structure. These exercises have been integrated into the structural geology curriculum and made available on the web through the KeckCAVES Education website as both data-and-code downloads and pre-made movies. One of the main challenges of implementing research and education activities through the award is that progress must be made on both throughout the award period. Therefore, while our original intent was to use subduction model output as the structures in the educational models, delays in the research results required that we develop these models using other simpler input data sets. These delays occurred because one of the other goals of the CAREER grant is to allow the faculty to take their research in a new direction, which may certainly lead to transformative science, but can also lead to more false-starts as the challenges of doing the new science are overcome. However, having created the infrastructure for the educational components, use of the model results in future

  6. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

    PubMed Central

    Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador

    2015-01-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144

  7. New software for visualizing 3D geological data in coal mines

    NASA Astrophysics Data System (ADS)

    Lee, Sungjae; Choi, Yosoon

    2015-04-01

    This study developed new software to visualize 3D geological data in coal mines. The Visualization Tool Kit (VTK) library and Visual Basic.NET 2010 were used to implement the software. The software consists of several modules providing functionalities: (1) importing and editing borehole data; (2) modelling of coal seams in 3D; (3) modelling of coal properties using 3D ordinary Kriging method; (4) calculating economical values of 3D blocks; (5) pit boundary optimization for identifying economical coal reserves based on the Lerchs-Grosmann algorithm; and (6) visualizing 3D geological, geometrical and economical data. The software has been applied to a small-scale open-pit coal mine in Indonesia revealed that it can provide useful information supporting the planning and design of open-pit coal mines.

  8. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    PubMed Central

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  9. Development of a geological 3D-model for improved calculations of groundwater vulnerability

    NASA Astrophysics Data System (ADS)

    Lerch, C.; Hoppe, A.

    2007-06-01

    The role and function of the unsaturated zone in groundwater protection is a basic question in land use planning. To quantify this protective ability, different approaches have been adopted which focus on various issues including the water retention period, behavior of organic components or amount of infiltration water available. Most methods use information from drill logs and interpolate the point data to delineate a groundwater protection map. In some cases the dimensions of the geological structures are considered, but often the spatial structure is disregarded. In this paper, a method is introduced which combines the development of a 3D geological model and the application of a standard method for computing groundwater vulnerability. Thus a spatially-continuous evaluation of groundwater protection is possible. As a test case, a spatial geological model was set up at a site southeast of Frankfurt am Main, Germany. The result was used to compute and map the local groundwater vulnerability. The result was compared with interpolated maps from drill data.

  10. Methods of constructing a 3D geological model from scatter data

    SciTech Connect

    Horsman, J.; Bethel, W.

    1995-04-01

    Most geoscience applications, such as assessment of an oil reservoir or hazardous waste site, require geological characterization of the site. Geological characterization involves analysis of spatial distributions of lithology, porosity, etc. Because of the complexity of the spatial relationships, the authors find that a 3-D model of geology is better suited for integration of many different types of data and provides a better representation of a site than a 2-D one. A 3-D model of geology is constructed from sample data obtained from field measurements, which are usually scattered. To create a volume model from scattered data, interpolation between points is required. The interpolation can be computed using one of several computational algorithms. Alternatively, a manual method may be employed, in which an interactive graphics device is used to input by hand the information that lies between the data points. For example, a mouse can be used to draw lines connecting data points with equal values. The combination of these two methods presents yet another approach. In this study, the authors will compare selected methods of 3-D geological modeling, They used a flow-based, modular visualization environment (AVS) to construct the geological models computationally. Within this system, they used three modules, scat{_}3d, trivar and scatter{_}to{_}ucd, as examples of computational methods. They compare these methods to the combined manual and computational approach. Because there are no tools readily available in AVS for this type of construction, they used a geological modeling system to demonstrate this method.

  11. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling. PMID:26689764

  12. Estimation of uncertainties in geological 3D raster layer models as integral part of modelling procedures

    NASA Astrophysics Data System (ADS)

    Maljers, Denise; den Dulk, Maryke; ten Veen, Johan; Hummelman, Jan; Gunnink, Jan; van Gessel, Serge

    2016-04-01

    The Geological Survey of the Netherlands (GSN) develops and maintains subsurface models with regional to national coverage. These models are paramount for petroleum exploration in conventional reservoirs, for understanding the distribution of unconventional reservoirs, for mapping geothermal aquifers, for the potential to store carbon, or for groundwater- or aggregate resources. Depending on the application domain these models differ in depth range, scale, data used, modelling software and modelling technique. Depth uncertainty information is available for the Geological Survey's 3D raster layer models DGM Deep and DGM Shallow. These models cover different depth intervals and are constructed using different data types and different modelling software. Quantifying the uncertainty of geological models that are constructed using multiple data types as well as geological expert-knowledge is not straightforward. Examples of geological expert-knowledge are trend surfaces displaying the regional thickness trends of basin fills or steering points that are used to guide the pinching out of geological formations or the modelling of the complex stratal geometries associated with saltdomes and saltridges. This added a-priori knowledge, combined with the assumptions underlying kriging (normality and second-order stationarity), makes the kriging standard error an incorrect measure of uncertainty for our geological models. Therefore the methods described below were developed. For the DGM Deep model a workflow has been developed to assess uncertainty by combining precision (giving information on the reproducibility of the model results) and accuracy (reflecting the proximity of estimates to the true value). This was achieved by centering the resulting standard deviations around well-tied depths surfaces. The standard deviations are subsequently modified by three other possible error sources: data error, structural complexity and velocity model error. The uncertainty workflow

  13. Visualization and dissemination of 3D geological property models of the Netherlands

    NASA Astrophysics Data System (ADS)

    Stafleu, Jan; Sobisch, Hans-Georg; Maljers, Denise; Hummelman, Jan; Dambrink, Roula M.; Gunnink, Jan L.

    2013-04-01

    The Geological Survey of the Netherlands (GSN) systematically produces 3D geological models of the Netherlands. To date, we build and maintain two different types of nation-wide models: (1) layer-based models in which the subsurface is represented by a series of tops and bases of geological or hydrogeological units, and (2) voxel models in which the subsurface is subdivided in a regular grid of voxels that can contain different properties. Our models are disseminated free-of-charge through the DINO-portal (www.dinoloket.nl) in a number of ways, including in an on-line map viewer with the option to create vertical cross-sections through the models, and as a series of downloadable GIS products. A recent addition to the portal is the freely downloadable SubsurfaceViewer software (developed by INSIGHT GmbH), allowing users to download and visualize both the layer-based models and the voxel models on their desktop computers. The SubsurfaceViewer allows visualization and analysis of geological layer-based and voxel models of different data structures and origin and includes a selection of data used to construct the respective model (maps, cross-sections, borehole data, etc.). The user is presented both a classical map view and an interactive 3D view. In addition, the SubsurfaceViewer offers a one dimensional vertical view as a synthetic borehole as well as a vertical cross-section view. The data structure is based on XML and linked ASCII-files and allows the hybrid usage of layers (tin and 2D raster) and voxels (3D raster). A recent development in the SubsurfaceViewer is the introduction of a data structure supporting irregular voxels. We have chosen a simple data structure consisting of a plain ASCII-file containing the x,y,z -coordinates of the lower left and upper right corner of each voxel followed by a list of property values (e.g. the geological unit the voxel belongs to, the lithological composition and the hydraulic conductivity). Irregular voxels are used to

  14. Uncertainty analysis for 3D geological modeling using the Kriging variance

    NASA Astrophysics Data System (ADS)

    Choi, Yosoon; Choi, Younjung; Park, Sebeom; Um, Jeong-Gi

    2014-05-01

    The credible estimation of geological properties is critical in many geosciences fields including the geotechnical engineering, environmental engineering, mining engineering and petroleum engineering. Many interpolation techniques have been developed to estimate the geological properties from limited sampling data such as borehole logs. The Kriging is an interpolation technique that gives the best linear unbiased prediction of the intermediate values. It also provides the Kriging variance which quantifies the uncertainty of the kriging estimates. This study provides a new method to analyze the uncertainty in 3D geological modeling using the Kriging variance. The cut-off values determined by the Kriging variance were used to effectively visualize the 3D geological models with different confidence levels. This presentation describes the method for uncertainty analysis and a case study which evaluates the amount of recoverable resources by considering the uncertainty.

  15. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

    The traditional approach used in modeling of composites reinforced by three-dimensional (3-D) braids is to assume a simple unit cell geometry of a 3-D braided structure with known fiber volume fraction and orientation. In this article, we first examine 3-D braiding methods in the light of braid structures, followed by the development of geometric models for 3-D braids using a unit cell approach. The unit cell geometry of 3-D braids is identified and the relationship of structural parameters such as yarn orientation angle and fiber volume fraction with the key processing parameters established. The limiting geometry has been computed by establishing the point at which yarns jam against each other. Using this factor makes it possible to identify the complete range of allowable geometric arrangements for 3-D braided preforms. This identified unit cell geometry can be translated to mechanical models which relate the geometrical properties of fabric preforms to the mechanical responses of composite systems.

  16. 3D Seismic Reflection Data: Has the Geological Hubble Retained Its Focus?

    NASA Astrophysics Data System (ADS)

    Jackson, Christopher

    2016-04-01

    In their seminal paper in 2002, Joe Cartwright and Mads Huuse referred to 3D seismic reflection data as the 'Geological Hubble', illustrating how these data had the potential to revolutionise our understanding of the genesis and evolution of sedimentary basins. 14 years on, I will here outline just some of the key recent advances made in our understanding of basin structure and stratigraphy, focusing on: (i) the intrusion and extrusion of igneous rocks; (ii) salt tectonics, with particular emphasis on intrasalt structure and the kinematics and mechanics of diapirism; (iii) the geometry and growth of normal faults; and (iv) the structure and emplacement of mass-transport complexes (MTCs). I will stress that future advances at least partly relies on hydrocarbon exploration companies and government agencies continuing to make their data freely available via easy-to-access data portals. I will issue a clarion call to academics, stressing that 'geodynamicists', sedimentologists, structural geologists and geomorphologists, amongst others, can benefit from utilising what I believe are currently an underused data type.

  17. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

    The achievement of volume geometry data from middle ear structures and surrounding components performs a necessary supposition for the finite element simulation of the vibrational and transfer characteristics of the ossicular chain. So far those models base on generalized figures and size data from anatomy textbooks or particular manual and one- or two-dimensional distance measurements of single ossicles, mostly obtained by light microscopy, respectively. Therefore the goal of this study is to create a procedure for complete three-dimensional imaging of real middle ear structures (tympanic membrane, ossicles, ligaments) in vitro or even in vivo. The main problems are their microscopic size with relevant structures from 10 micrometer to 5 mm, representing various tissue properties (bone, soft tissue). Additionally, these structures are surrounded by the temporal bone, the most solid bone of the human body. Generally there exist several established diagnostic tools for medical imaging that could be used for geometry data acquisition, e.g., X-ray computed tomography and magnetic resonance imaging. Basically they image different tissue parameters, either bony structures (ossicles), or soft tissue (tympanic membrane, ligaments). But considering this application those standard techniques allow low spatial resolution only, usually in the 0.5 - 1mm range, at least in one spatial direction. Thus particular structures of the middle ear region could even be missed completely because of their spatial location. In vitro there is a way out by collecting three complete data sets, each distinguished by 90 degree rotation of a cube-shaped temporal bone specimen. That allows high-resolution imaging in three orthogonal planes, which essentially supports the three-dimensional interpolation of the unknown elements, starting from the regularly set elements of the cubic grid with an edge extension given by the original two-dimensional matrix. A different approach represents the

  18. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

    Dvir, Hay; Silman, Israel; Harel, Michal; Rosenberry, Terrone L.; Sussman, Joel L.

    2010-01-01

    By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer’s disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge. PMID:20138030

  19. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

    Gritto, Roland; O'Connell, Daniel; Elobaid Elnaiem, Ali; Mohamed, Fathelrahman; Sadooni, Fadhil

    2016-04-01

    The Middle-East has seen a recent boom in construction including the planning and development of complete new sub-sections of metropolitan areas. Before planning and construction can commence, however, the development areas need to be investigated to determine their suitability for the planned project. Subsurface parameters such as the type of material (soil/rock), thickness of top soil or rock layers, depth and elastic parameters of basement, for example, comprise important information needed before a decision concerning the suitability of the site for construction can be made. A similar problem arises in environmental impact studies, when subsurface parameters are needed to assess the geological heterogeneity of the subsurface. Environmental impact studies are typically required for each construction project, particularly for the scale of the aforementioned building boom in the Middle East. The current study was conducted in Qatar at the location of a future highway interchange to evaluate a suite of 3D seismic techniques in their effectiveness to interrogate the subsurface for the presence of karst-like collapse structures. The survey comprised an area of approximately 10,000 m2 and consisted of 550 source- and 192 receiver locations. The seismic source was an accelerated weight drop while the geophones consisted of 3-component 10 Hz velocity sensors. At present, we analyzed over 100,000 P-wave phase arrivals and performed high-resolution 3-D tomographic imaging of the shallow subsurface. Furthermore, dispersion analysis of recorded surface waves will be performed to obtain S-wave velocity profiles of the subsurface. Both results, in conjunction with density estimates, will be utilized to determine the elastic moduli of the subsurface rock layers.

  20. A 3D geological model of 67P Churyumov-Gerasimenko northern hemisphere

    NASA Astrophysics Data System (ADS)

    Massironi, Matteo; Penasa, Luca; Simioni, Emanuele; Naletto, Giampiero; Cremonese, Gabriele

    2016-04-01

    Stratification appears to be widespread and continuous on the North hemisphere of comet 67P/ Churyumov-Gerasimenko which has been observed by the Rosetta probe since August 2014 (Massironi et al. 2015). This allowed us to reconstruct the true 3D subsurface geology of most of the inner structure of the comet nucleus on the basis of the OSIRIS (Optical, Spectroscopic, and Infrared Remote Imaging System) observation and the derived photogrammetric and photo-clinometric shape models. We intend to populate the geo-model with the physical properties assumed for the cometary interior (porosity, density, strength and volatile content) and eventually use it as a base to interpret the radar sounding results obtained by CONSERT (Comet Nucleus Sounding Experiment by Radiowave Transmission observations) (e.g. Ciarletti et al. 2015). This would give us important hints on the distribution and geometry of primordial structures within the comet interior. Massironi M. et al. 2015, Nature, 526, 402-405. Ciarletti V. et al. 2015, Astronomy & Astrophysic, no. aa26337-15

  1. Quality control of 3D Geological Models using an Attention Model based on Gaze

    NASA Astrophysics Data System (ADS)

    Busschers, Freek S.; van Maanen, Peter-Paul; Brouwer, Anne-Marie

    2014-05-01

    The Geological Survey of the Netherlands (GSN) produces 3D stochastic geological models of the upper 50 meters of the Dutch subsurface. The voxel models are regarded essential in answering subsurface questions on, for example, aggregate resources, groundwater flow, land subsidence studies and the planning of large-scale infrastructural works such as tunnels. GeoTOP is the most recent and detailed generation of 3D voxel models. This model describes 3D lithological variability up to a depth of 50 m using voxels of 100*100*0.5m. Due to the expected increase in data-flow, model output and user demands, the development of (semi-)automated quality control systems is getting more important in the near future. Besides numerical control systems, capturing model errors as seen from the expert geologist viewpoint is of increasing interest. We envision the use of eye gaze to support and speed up detection of errors in the geological voxel models. As a first step in this direction we explore gaze behavior of 12 geological experts from the GSN during quality control of part of the GeoTOP 3D geological model using an eye-tracker. Gaze is used as input of an attention model that results in 'attended areas' for each individual examined image of the GeoTOP model and each individual expert. We compared these attended areas to errors as marked by the experts using a mouse. Results show that: 1) attended areas as determined from experts' gaze data largely match with GeoTOP errors as indicated by the experts using a mouse, and 2) a substantial part of the match can be reached using only gaze data from the first few seconds of the time geologists spend to search for errors. These results open up the possibility of faster GeoTOP model control using gaze if geologists accept a small decrease of error detection accuracy. Attention data may also be used to make independent comparisons between different geologists varying in focus and expertise. This would facilitate a more effective use of

  2. Comparison of protein structures using 3D profile alignment.

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

    A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025

  3. 3D constrained inversion of geophysical and geological information applying Spatial Mutually Constrained Inversion.

    NASA Astrophysics Data System (ADS)

    Nielsen, O. F.; Ploug, C.; Mendoza, J. A.; Martínez, K.

    2009-05-01

    The need for increaseding accuracy and reduced ambiguities in the inversion results has resulted in focus on the development of more advanced inversion methods of geophysical data. Over the past few years more advanced inversion techniques have been developed to improve the results. Real 3D-inversion is time consuming and therefore often not the best solution in a cost-efficient perspective. This has motivated the development of 3D constrained inversions, where 1D-models are constrained in 3D, also known as a Spatial Constrained Inversion (SCI). Moreover, inversion of several different data types in one inversion has been developed, known as Mutually Constrained Inversion (MCI). In this paper a presentation of a Spatial Mutually Constrained Inversion method (SMCI) is given. This method allows 1D-inversion applied to different geophysical datasets and geological information constrained in 3D. Application of two or more types of geophysical methods in the inversion has proved to reduce the equivalence problem and to increase the resolution in the inversion results. The use of geological information from borehole data or digital geological models can be integrated in the inversion. In the SMCI, a 1D inversion code is used to model soundings that are constrained in three dimensions according to their relative position in space. This solution enhances the accuracy of the inversion and produces distinct layers thicknesses and resistivities. It is very efficient in the mapping of a layered geology but still also capable of mapping layer discontinuities that are, in many cases, related to fracturing and faulting or due to valley fills. Geological information may be included in the inversion directly or used only to form a starting model for the individual soundings in the inversion. In order to show the effectiveness of the method, examples are presented from both synthetic data and real data. The examples include DC-soundings as well as land-based and airborne TEM

  4. Analysis of Geological Structures

    NASA Astrophysics Data System (ADS)

    Price, Neville J.; Cosgrove, John W.

    1990-08-01

    A knowledge of structural geology is fundamental to understanding the processes by which the earth's crust has evolved. It is a subject of fundamental importance to students of geology, experienced field geologists and academic researchers as well as to petroleum and mining engineers. In contrast to many structural textbooks which dwell upon geometrical descriptions of geological structures, this book emphasises mechanical principles and the way in which they can be used to understand how and why a wide range of geological structures develop. Structures on all scales are considered but the emphasis of the book is on those that can be seen on the scale of hand specimen or outcrop. Drawing on their considerable teaching experience the authors present a coherent and lucid analysis of geological structures which will be welcomed by a wide variety of earth scientists.

  5. Estimating the complexity of 3D structural models using machine learning methods

    NASA Astrophysics Data System (ADS)

    Mejía-Herrera, Pablo; Kakurina, Maria; Royer, Jean-Jacques

    2016-04-01

    Quantifying the complexity of 3D geological structural models can play a major role in natural resources exploration surveys, for predicting environmental hazards or for forecasting fossil resources. This paper proposes a structural complexity index which can be used to help in defining the degree of effort necessary to build a 3D model for a given degree of confidence, and also to identify locations where addition efforts are required to meet a given acceptable risk of uncertainty. In this work, it is considered that the structural complexity index can be estimated using machine learning methods on raw geo-data. More precisely, the metrics for measuring the complexity can be approximated as the difficulty degree associated to the prediction of the geological objects distribution calculated based on partial information on the actual structural distribution of materials. The proposed methodology is tested on a set of 3D synthetic structural models for which the degree of effort during their building is assessed using various parameters (such as number of faults, number of part in a surface object, number of borders, ...), the rank of geological elements contained in each model, and, finally, their level of deformation (folding and faulting). The results show how the estimated complexity in a 3D model can be approximated by the quantity of partial data necessaries to simulated at a given precision the actual 3D model without error using machine learning algorithms.

  6. Handling and quantifying uncertainty in geological 3D models: A methodological approach based on remote-sensing and field work.

    NASA Astrophysics Data System (ADS)

    Baumberger, Roland; Wehrens, Philip; Herwegh, Marco

    2013-04-01

    Geological 3D models are always just an approximation of a complex natural situation. This is especially true in regions, where hard underground data (e.g. bore holes, tunnel mappings and seismic data) is lacking. One of the key problems while developing valid geological 3D models is the three-dimensional spatial distribution of geological structures, particularly with increasing distance from the surface. In our study, we investigate the Alpine 3D Deformation of the crystalline rocks of the Aar massif (Haslital valley, Central Switzerland). Deformation in this area is dominated by different sets of large-scale shear zones, which acted under both ductile and brittle deformation conditions. The goal of our study is the prediction of the geometry and the evolution of the structures in 3D space and time. A key point in our project is the generation of a reliable 3D model of today's structures. In this sense, estimation of the reliability of the surface information for the extrapolation to depth is mandatory. Based on our data, a method will be presented that contributes to a possible solution of the questions addressed above. The basic idea consists of the fact that (i) mechanical anisotropies as shear zones and faults show prominent three-dimensional information in the landscape, (ii) these geometries can be used as input data for a geological 3D model and (iii) that the 3D information mentioned allows a projection to depth. As a great advantage of the study area, a large number of underground tunnels exist, which allow to evaluate the quality of the aforementioned extrapolations. The method is based on a combined remote-sensing and field work approach: morphological incisions recognized on digital elevation models as well as on aerial photos on the computer screen were evaluated, described and attributed in detail in the field. Our approach is based on a six step workflow: (1) Elaboration of a large-scale structural map of geological structures by means of remote

  7. Joint 3D inversion of gravity and magnetic data with geological constraints - an alternative approach

    NASA Astrophysics Data System (ADS)

    Prutkin, Ilya; Vajda, Peter; Jentzsch, Gerhard

    2016-04-01

    Quite a popular approach now by interpretation of gravity data is a linear one - an attempt is made to find a density distribution d(x,y,z) below the Earth's surface. This approach has clear disadvantages. First, we face the problem of dimensionality: one looks for 3D function based on 2D data set (measurements on the Earth's surface), the degree of non-uniqueness is extremely high, and no regularization can save the situation. The number of unknowns is many times higher than the number of observations; otherwise, we obtain a very rough model of the lower half-space. Second, the linear approach is not reasonable from the geological point of view. It implies that density varies from one point to another. Usually, we assume big volumes with nearly homogeneous density - layers, blocks, intrusions. It looks more understandable, to search for geometry of density interfaces: 3D topography of contact surfaces and shapes of restricted bodies (intrusions). Third, in the framework of the linear approach even for a synthetic field of two separate objects we obtain clouds of points with slightly increased density. It is hardly ever possible, to isolate objects, particularly when one of them is located above another one. We suggest an alternative approach for the linear one. Our approach has been successfully applied for several case histories including a local gravity anomaly Kolarovo and a bigger area of the Thuringian Basin, where both gravity and magnetic data are inverted. First, we separate sources into deep, intermediate and shallow ones, using subsequent upward and downward continuation. All components are inverted separately. We address a problem which we name the problem of low frequencies: deep objects generate long wavelengths, but the converse implication is not necessarily true. For instance, the effect of the basin structure contributes substantially into low frequencies, though it is caused by shallow sources. However, our numerical experiments with intermediate

  8. Facets : a Cloudcompare Plugin to Extract Geological Planes from Unstructured 3d Point Clouds

    NASA Astrophysics Data System (ADS)

    Dewez, T. J. B.; Girardeau-Montaut, D.; Allanic, C.; Rohmer, J.

    2016-06-01

    Geological planar facets (stratification, fault, joint…) are key features to unravel the tectonic history of rock outcrop or appreciate the stability of a hazardous rock cliff. Measuring their spatial attitude (dip and strike) is generally performed by hand with a compass/clinometer, which is time consuming, requires some degree of censoring (i.e. refusing to measure some features judged unimportant at the time), is not always possible for fractures higher up on the outcrop and is somewhat hazardous. 3D virtual geological outcrop hold the potential to alleviate these issues. Efficiently segmenting massive 3D point clouds into individual planar facets, inside a convenient software environment was lacking. FACETS is a dedicated plugin within CloudCompare v2.6.2 (http://cloudcompare.org/ ) implemented to perform planar facet extraction, calculate their dip and dip direction (i.e. azimuth of steepest decent) and report the extracted data in interactive stereograms. Two algorithms perform the segmentation: Kd-Tree and Fast Marching. Both divide the point cloud into sub-cells, then compute elementary planar objects and aggregate them progressively according to a planeity threshold into polygons. The boundaries of the polygons are adjusted around segmented points with a tension parameter, and the facet polygons can be exported as 3D polygon shapefiles towards third party GIS software or simply as ASCII comma separated files. One of the great features of FACETS is the capability to explore planar objects but also 3D points with normals with the stereogram tool. Poles can be readily displayed, queried and manually segmented interactively. The plugin blends seamlessly into CloudCompare to leverage all its other 3D point cloud manipulation features. A demonstration of the tool is presented to illustrate these different features. While designed for geological applications, FACETS could be more widely applied to any planar

  9. Geological characterisation of complex reservoirs using 3D seismic: Case studies

    NASA Astrophysics Data System (ADS)

    Benaissa, Zahia; Benaïssa, Abdelkader; Seghir Baghaoui, Mohamed; Bendali, Mohamed; Chami, Adel; Khelifi Touhami, Médina; Ouadfeul, Sid Ali; Boudella, Amar

    2014-05-01

    3D seismic allows getting a set of numerous closely-spaced seismic lines that provide a high spatially sampled measure of subsurface reflectivity. It leads to an accurate interpretation of seismic reflection data, which is one of the most important stages of a successful hydrocarbons exploration, especially in the reservoirs characterised by complex geological setting. We present here two case studies pertaining to two Algerian hydrocarbon fields. Considering the positive results obtained from 2D seismic interpretation, several wells were drilled. Some of them have proved dry, due certainly to inaccurate seismic interpretation because of non standard geological context. For the first case, the high quality of the 3D seismic data allowed to reveal, on all the inlines and crosslines, the existence of paleovalleys under the top of the Ordovician (unit IV) reservoir. The mapping of these paleovalleys clearly showed that the dry well, contrary to the other wells, was implanted outside paleovalleys. This fact was confirmed by the analysis of well data. The second case study concerns the problem of andesitic eruptive deposits on the top of the Ordovician reservoir, which condition the geometry and continuity of this reservoir and cause uncertainties in the mapping of the Hercynian unconformity. Well data associated with 3D seismic response shows that eruptive deposits generate high impedance anomaly because of the high density and velocity of andesites. We used this information to interpret these eruptive rocks as being responsible of high impedance anomalies, inside the Ordovician reservoir, on the impedance volume generated from the 3D seismic data. A 3D extraction of the anomalies allowed an accurate localisation of the andesites. So, it appears, according to these two case studies, that for an efficient recovery of hydrocarbons, we have to rely, first of all, on an accurate seismic interpretation before we use microscopic measurements. 3D seismic, once again, remains

  10. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

    Cartwright, D.; Csanak, G.; George, D.; Walker, R.; Kuprat, A.; Dengi, A.; Grobman, W.

    1999-06-01

    A new tool has been developed for calculating the capacitance matrix for complex 3D interconnect structures involving multiple layers of irregularly shaped interconnect, imbedded in different dielectric materials. This method utilizes a new 3D adaptive unstructured grid capability, and a linear finite element algorithm. The capacitance is determined from the minimum in the total system energy as the nodes are varied to minimize the error in the electric field in the dielectric(s).

  11. Fundamentals of Structural Geology

    NASA Astrophysics Data System (ADS)

    Pollard, David D.; Fletcher, Raymond C.

    2005-09-01

    Fundamentals of Structural Geology provides a new framework for the investigation of geological structures by integrating field mapping and mechanical analysis. Assuming a basic knowledge of physical geology, introductory calculus and physics, it emphasizes the observational data, modern mapping technology, principles of continuum mechanics, and the mathematical and computational skills, necessary to quantitatively map, describe, model, and explain deformation in Earth's lithosphere. By starting from the fundamental conservation laws of mass and momentum, the constitutive laws of material behavior, and the kinematic relationships for strain and rate of deformation, the authors demonstrate the relevance of solid and fluid mechanics to structural geology. This book offers a modern quantitative approach to structural geology for advanced students and researchers in structural geology and tectonics. It is supported by a website hosting images from the book, additional colour images, student exercises and MATLAB scripts. Solutions to the exercises are available to instructors. The book integrates field mapping using modern technology with the analysis of structures based on a complete mechanics MATLAB is used to visualize physical fields and analytical results and MATLAB scripts can be downloaded from the website to recreate textbook graphics and enable students to explore their choice of parameters and boundary conditions The supplementary website hosts color images of outcrop photographs used in the text, supplementary color images, and images of textbook figures for classroom presentations The textbook website also includes student exercises designed to instill the fundamental relationships, and to encourage the visualization of the evolution of geological structures; solutions are available to instructors

  12. Taking geoscience to the IMAX: 3D and 4D insight into geological processes using micro-CT

    NASA Astrophysics Data System (ADS)

    Dobson, Katherine; Dingwell, Don; Hess, Kai-Uwe; Withers, Philip; Lee, Peter; Pistone, Mattia; Fife, Julie; Atwood, Robert

    2015-04-01

    Geology is inherently dynamic, and full understanding of any geological system can only be achieved by considering the processes by which change occurs. Analytical limitations mean understanding has largely developed from ex situ analyses of the products of geological change, rather than of the processes themselves. Most methods essentially utilise "snap shot" sampling: and from thin section petrography to high resolution crystal chemical stratigraphy and field volcanology, we capture an incomplete view of a spatially and temporally variable system. Even with detailed experimental work, we can usually only analyse samples before and after we perform an experiment, as routine analysis methods are destructive. Serial sectioning and quenched experiments stopped at different stages can give some insight into the third and fourth dimension, but the true scaling of the processes from the laboratory to the 4D (3D + time) geosphere is still poorly understood. Micro computed tomography (XMT) can visualise the internal structures and spatial associations within geological samples non-destructively. With image resolutions of between 200 microns and 50 nanometres, tomography has the ability to provide a detailed sample assessment in 3D, and quantification of mineral associations, porosity, grain orientations, fracture alignments and many other features. This allows better understanding of the role of the complex geometries and associations within the samples, but the challenge of capturing the processes that generate and modify these structures remains. To capture processes, recent work has focused on developing experimental capability for in situ experiments on geological materials. Data presented will showcase examples from recent experiments where high speed synchrotron x-ray tomography has been used to acquire each 3D image in under 2 seconds. We present a suite of studies that showcase how it is now possible to take quantification of many geological processed into 3D and

  13. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  14. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

    Campbell, Leckey Cara A/; Miler, Corey A.; Hinders, Mark K.

    2011-01-01

    Structural health monitoring (SHM) for the detection of damage in aerospace materials is an important area of research at NASA. Ultrasonic guided Lamb waves are a promising SHM damage detection technique since the waves can propagate long distances. For complicated flaw geometries experimental signals can be difficult to interpret. High performance computing can now handle full 3-dimensional (3D) simulations of elastic wave propagation in materials. We have developed and implemented parallel 3D elastodynamic finite integration technique (3D EFIT) code to investigate ultrasound scattering from flaws in materials. EFIT results have been compared to experimental data and the simulations provide unique insight into details of the wave behavior. This type of insight is useful for developing optimized experimental SHM techniques. 3D EFIT can also be expanded to model wave propagation and scattering in anisotropic composite materials.

  15. Stratigraphy and structural geology

    NASA Technical Reports Server (NTRS)

    Carr, M. H.; Wilhelms, D. E.; Greeley, R.; Guest, J. E.

    1976-01-01

    The immediate goal of stratigraphy and structural geology is to reduce the enormous complexity of a planetary surface to comprehensible proportions by dividing the near-surface rocks into units and mapping their distribution and attitude.

  16. Modeling 3D soil and sediment distributions for assessing catchment structure and hydrological feedbacks

    NASA Astrophysics Data System (ADS)

    Maurer, Thomas; Brück, Yasemine; Hinz, Christoph; Gerke, Horst H.

    2015-04-01

    Structural heterogeneity, namely the spatial distribution of soils and sediments (represented by mineral particles), characterizes catchment hydrological behavior. In natural catchments, local geology and the specific geomorphic processes determine the characteristics and spatial distribution of structures. In constructed catchments, structural features are determined primarily by the construction processes and the geological origin of the parent material. Objectives are scenarios of 3D catchment structures in form of complete 3D description of soil hydraulic properties generated from the knowledge of the formation processes. The constructed hydrological catchment 'Hühnerwasser' (Lower Lusatia, Brandenburg, Germany) was used for the calibration and validation of model results due to its well-known conditions. For the modelling of structural features, a structure generator was used to model i) quasi-deterministic sediment distributions using input data from a geological model of the parent material excavation site; ii) sediment distributions that are conditioned to measurement data from soil sampling; and iii) stochastic component sediment distributions. All three approaches allow a randomization within definable limits. Furthermore, the spoil cone / spoil ridge orientation, internal layering, surface compaction and internal spoil cone compaction were modified. These generated structural models were incorporated in a gridded 3D volume model constructed with the GOCAD software. For selected scenarios, the impact of structure variation was assessed by hydrological modelling with HYDRUS 2D/3D software. For that purpose, 3D distributions of soil hydraulic properties were estimated based on generated sediment properties using adapted pedotransfer functions. Results from the hydrological model were compared them to measured discharges from the catchment. The impact of structural feature variation on flow behaviour was analysed by comparing different simulation scenarios

  17. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

    Gong, Xingting; Cho, Yigil; Castle, Toen; Sussman, Daniel; Kamien, Randall

    2015-03-01

    The purpose of this talk is to explore how one can create 3D structures from 2D materials through the art of kirigami. Kirigami expands upon origami by allowing not only folds, but also cuts, into materials. If we take an incompressible material such as paper and remove a hole from it, the paper will buckle into the third dimension once that hole is sealed in order to relieve strain. Thus, orienting cuts and folds in certain places throughout a sheet of paper can influence its ``pop-up,'' 3D structure. To narrow down the inverse design problem, we confined ourselves to making only one kind of cut (which we call the ``5-7 cut'') on a honeycomb grid, and we show how this single cut can give rise to arbitrarily complex three dimensional structures. A simple set of rules exists: (a) one 5-7 cut divides the material into 2 sections which can choose to pop-up or down independently of each other, (b) rows of uniform cuts must pop up or down in unison, giving (nearly) arbitrary 2D structure, and (c) the 5-7 cuts can be arranged in various ways to create 6 basic pop-up ``modes,'' which can then be arranged to give (nearly) arbitrary 3D structure. These simple rules allow a framework for designing targeted 3D structure from an initial 2D sheet of material. This work was supported by NSF EFRI-ODISSEI Grant EFRI 13-31583.

  18. Digital mono- and 3D stereo-photogrammetry for geological and geomorphological mapping

    NASA Astrophysics Data System (ADS)

    Scapozza, Cristian; Schenker, Filippo Luca; Castelletti, Claudio; Bozzini, Claudio; Ambrosi, Christian

    2016-04-01

    The generalization of application of digital tools for managing, mapping and updating geological data have become widely accepted in the last decennia. Despite the increasing quality and availability of digital topographical maps, orthorectified aerial photographs (orthophotos) and high resolution (5 up to 0.5 m) Digital Elevation Models (DEMs), a correct recognition of the kind, the nature and the boundaries of geological formations and geomophological landforms, unconsolidated sedimentary deposits or slope instabilities is often very difficult on conventional two-dimensional (2D) products, in particular in steep zones (rock walls and talus slopes), under the forest cover, for a very complex topography and in deeply urbanised zones. In many cases, photo-interpretative maps drawn only by 2D data sets must be improved by field verifications or, at least, by field oblique photographs. This is logical, because our natural perception of the real world is three-dimensional (3D), which is partially disabled by the application of 2D visualization techniques. Here we present some examples of application of digital mapping based on a 3D visualization (for aerial and satellite images photo-interpretation) or on a terrestrial perception by digital mono-photogrammetry (for oblique photographs). The 3D digital mapping was performed thanks to an extension of the software ESRI® ArcGIS™ called ArcGDS™. This methodology was also applied on historical aerial photographs (normally analysed by optical stereo-photogrammetry), which were digitized by scanning and then oriented and aero-triangulated thanks to the ArcGDS™ software, allowing the 3D visualisation and the mapping in a GIS environment (Ambrosi and Scapozza, 2015). The mono-photogrammetry (or monoplotting) is the technique of photogrammetrical georeferentiation of single oblique unrectified photographs, which are related to a DEM. In other words, the monoplotting allows relating each pixel of the photograph to the

  19. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  20. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures

    PubMed Central

    Rahrig, Ryan R.; Petrov, Anton I.; Leontis, Neocles B.; Zirbel, Craig L.

    2013-01-01

    The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/. PMID:23716643

  1. RNAComposer and RNA 3D structure prediction for nanotechnology.

    PubMed

    Biesiada, Marcin; Pachulska-Wieczorek, Katarzyna; Adamiak, Ryszard W; Purzycka, Katarzyna J

    2016-07-01

    RNAs adopt specific, stable tertiary architectures to perform their activities. Knowledge of RNA tertiary structure is fundamental to understand RNA functions beginning with transcription and ending with turnover. Contrary to advanced RNA secondary structure prediction algorithms, which allow good accuracy when experimental data are integrated into the prediction, tertiary structure prediction of large RNAs still remains a significant challenge. However, the field of RNA tertiary structure prediction is rapidly developing and new computational methods based on different strategies are emerging. RNAComposer is a user-friendly and freely available server for 3D structure prediction of RNA up to 500 nucleotide residues. RNAComposer employs fully automated fragment assembly based on RNA secondary structure specified by the user. Importantly, this method allows incorporation of distance restraints derived from the experimental data to strengthen the 3D predictions. The potential and limitations of RNAComposer are discussed and an application to RNA design for nanotechnology is presented. PMID:27016145

  2. 3D unconstrained and geologically constrained stochastic inversion of airborne vertical gravity gradient data

    NASA Astrophysics Data System (ADS)

    Tchikaya, Euloge Budet; Chouteau, Michel; Keating, Pierre; Shamsipour, Pejman

    2016-02-01

    We present an inversion tool for airborne gravity gradient data that yields a 3D density model using stochastic methods i.e. cokriging and conditional simulation. This method uses geostatistical properties of the measured gravity gradient to estimate a 3D density model whose gravity response fits the measured gravity gradient anomaly. Linearity between gravity gradient data and density allows estimation of the model (density) covariance using observed data, i.e. we adjust iteratively the density covariance matrix by fitting experimental and theoretical gravity gradient covariance matrices. Inversion can be constrained by including densities known at some locations. In addition we can explore various reasonable solutions that honour both the estimated density covariance model and the gravity gradient data using geostatistical simulation. The proposed method is first tested with two synthetic datasets generated from a sharp-boundary model and a smooth stochastic model respectively. The results show the method to be capable of retrieving models compatible with the true models; it also allows the integration of complex a priori information. The technique is then applied to gravity gradient survey data collected for the Geological Survey of Canada in the area of McFaulds Lake (Ontario, Canada) using the Falcon airborne gravity system. Unconstrained inversion returns a density model that is geologically plausible and the computed response exactly fits the observed gravity gradient anomaly.

  3. Constructing a large-scale 3D Geologic Model for Analysis of the Non-Proliferation Experiment

    SciTech Connect

    Wagoner, J; Myers, S

    2008-04-09

    We have constructed a regional 3D geologic model of the southern Great Basin, in support of a seismic wave propagation investigation of the 1993 Nonproliferation Experiment (NPE) at the Nevada Test Site (NTS). The model is centered on the NPE and spans longitude -119.5{sup o} to -112.6{sup o} and latitude 34.5{sup o} to 39.8{sup o}; the depth ranges from the topographic surface to 150 km below sea level. The model includes the southern half of Nevada, as well as parts of eastern California, western Utah, and a portion of northwestern Arizona. The upper crust is constrained by both geologic and geophysical studies, while the lower crust and upper mantle are constrained by geophysical studies. The mapped upper crustal geologic units are Quaternary basin fill, Tertiary deposits, pre-Tertiary deposits, intrusive rocks of all ages, and calderas. The lower crust and upper mantle are parameterized with 5 layers, including the Moho. Detailed geologic data, including surface maps, borehole data, and geophysical surveys, were used to define the geology at the NTS. Digital geologic outcrop data were available for both Nevada and Arizona, whereas geologic maps for California and Utah were scanned and hand-digitized. Published gravity data (2km spacing) were used to determine the thickness of the Cenozoic deposits and thus estimate the depth of the basins. The free surface is based on a 10m lateral resolution DEM at the NTS and a 90m lateral resolution DEM elsewhere. Variations in crustal thickness are based on receiver function analysis and a framework compilation of reflection/refraction studies. We used Earthvision (Dynamic Graphics, Inc.) to integrate the geologic and geophysical information into a model of x,y,z,p nodes, where p is a unique integer index value representing the geologic unit. For seismic studies, the geologic units are mapped to specific seismic velocities. The gross geophysical structure of the crust and upper mantle is taken from regional surface

  4. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Fang, Nicholas X.; Boyce, Mary C.

    2014-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the complex instability and wrinkling pattern arising in 3D structured composites and the effect of the buckling pattern on the overall structural response. The 3D structured composites consisted of stiffer plates supported by soft matrix on both sides. Compression beyond the critical strain led to complex buckling patterns in the initially straight plates. The motivation of our work is to elaborate the formation of a system of prescribed periodic scatterers (metamaterials) due to buckling, and their effect to interfere wave propagation through the metamaterial structures. Such metamaterials made from elastomers enable large reversible deformation and, as a result, significant changes of the wave propagation properties. We developed analytical and finite element models to capture various aspects of the instability mechanism. Mechanical experiments were designed to further explore the modeling results. The ability to actively alter the 3D composite structure can enable on-demand tunability of many different functions, such as active control of wave propagation to create band-gaps and waveguides.

  5. Structured Light-Based 3D Reconstruction System for Plants

    PubMed Central

    Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants.This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  6. Structured Light-Based 3D Reconstruction System for Plants.

    PubMed

    Nguyen, Thuy Tuong; Slaughter, David C; Max, Nelson; Maloof, Julin N; Sinha, Neelima

    2015-01-01

    Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance. PMID:26230701

  7. Lessons in modern digital field geology: Open source software, 3D techniques, and the new world of digital mapping

    NASA Astrophysics Data System (ADS)

    Pavlis, Terry; Hurtado, Jose; Langford, Richard; Serpa, Laura

    2014-05-01

    Although many geologists refuse to admit it, it is time to put paper-based geologic mapping into the historical archives and move to the full potential of digital mapping techniques. For our group, flat map digital geologic mapping is now a routine operation in both research and instruction. Several software options are available, and basic proficiency with the software can be learned in a few hours of instruction and practice. The first practical field GIS software, ArcPad, remains a viable, stable option on Windows-based systems. However, the vendor seems to be moving away from ArcPad in favor of mobile software solutions that are difficult to implement without GIS specialists. Thus, we have pursued a second software option based on the open source program QGIS. Our QGIS system uses the same shapefile-centric data structure as our ArcPad system, including similar pop-up data entry forms and generic graphics for easy data management in the field. The advantage of QGIS is that the same software runs on virtually all common platforms except iOS, although the Android version remains unstable as of this writing. A third software option we are experimenting with for flat map-based field work is Fieldmove, a derivative of the 3D-capable program Move developed by Midland Valley. Our initial experiments with Fieldmove are positive, particularly with the new, inexpensive (<300Euros) Windows tablets. However, the lack of flexibility in data structure makes for cumbersome workflows when trying to interface our existing shapefile-centric data structures to Move. Nonetheless, in spring 2014 we will experiment with full-3D immersion in the field using the full Move software package in combination with ground based LiDAR and photogrammetry. One new workflow suggested by our initial experiments is that field geologists should consider using photogrammetry software to capture 3D visualizations of key outcrops. This process is now straightforward in several software packages, and

  8. The Importance of Communicating Uncertainty to the 3D Geological Framework Model of Alberta

    NASA Astrophysics Data System (ADS)

    MacCormack, Kelsey

    2015-04-01

    The Alberta Geological Survey (AGS) has been tasked with developing a 3-dimensional (3D) geological framework for Alberta (660,000 km2). Our goal is to develop 'The Framework' as a sophisticated platform, capable of integrating a variety of data types from multiple sources enabling the development of multi-scale, interdisciplinary models with built-in feedback mechanisms, allowing the individual components of the model to adapt and evolve over time as our knowledge and understanding of the subsurface increases. The geoscience information within these models is often taken at face value and assumed that the attribute accuracy is equivalent to the digital accuracy recorded by the computer, which can lead to overconfidence in the model results. We need to make sure that decision makers understand that models are simply versions of reality and all contain a certain amount of error and uncertainty. More importantly, it is necessary to convey that error and uncertainty are not bad, and should be quantified and understood rather than ignored. This presentation will focus on how the AGS is quantifying and communicating uncertainty within the Geologic Framework to decision makers and the general public, as well as utilizing uncertainty results to strategically prioritize future work.

  9. Contribution of 3D inversion of Electrical Resistivity Tomography data applied to volcanic structures

    NASA Astrophysics Data System (ADS)

    Portal, Angélie; Fargier, Yannick; Lénat, Jean-François; Labazuy, Philippe

    2016-04-01

    The electrical resistivity tomography (ERT) method, initially developed for environmental and engineering exploration, is now commonly used for geological structures imaging. Such structures can present complex characteristics that conventional 2D inversion processes cannot perfectly integrate. Here we present a new 3D inversion algorithm named EResI, firstly developed for levee investigation, and presently applied to the study of a complex lava dome (the Puy de Dôme volcano, France). EResI algorithm is based on a conventional regularized Gauss-Newton inversion scheme and a 3D non-structured discretization of the model (double grid method based on tetrahedrons). This discretization allows to accurately model the topography of investigated structure (without a mesh deformation procedure) and also permits a precise location of the electrodes. Moreover, we demonstrate that a complete 3D unstructured discretization limits the number of inversion cells and is better adapted to the resolution capacity of tomography than a structured discretization. This study shows that a 3D inversion with a non-structured parametrization has some advantages compared to classical 2D inversions. The first advantage comes from the fact that a 2D inversion leads to artefacts due to 3D effects (3D topography, 3D internal resistivity). The second advantage comes from the fact that the capacity to experimentally align electrodes along an axis (for 2D surveys) depends on the constrains on the field (topography...). In this case, a 2D assumption induced by 2.5D inversion software prevents its capacity to model electrodes outside this axis leading to artefacts in the inversion result. The last limitation comes from the use of mesh deformation techniques used to accurately model the topography in 2D softwares. This technique used for structured discretization (Res2dinv) is prohibed for strong topography (>60 %) and leads to a small computational errors. A wide geophysical survey was carried out

  10. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

    Llewellyn-Jones, Thomas M.; Drinkwater, Bruce W.; Trask, Richard S.

    2016-02-01

    This paper shows the first application of in situ manipulation of discontinuous fibrous structure mid-print, within a 3D printed polymeric composite architecture. Currently, rapid prototyping methods (fused filament fabrication, stereolithography) are gaining increasing popularity within the engineering commnity to build structural components. Unfortunately, the full potential of these components is limited by the mechanical properties of the materials used. The aim of this study is to create and demonstrate a novel method to instantaneously orient micro-scale glass fibres within a selectively cured photocurable resin system, using ultrasonic forces to align the fibres in the desired 3D architecture. To achieve this we have mounted a switchable, focused laser module on the carriage of a three-axis 3D printing stage, above an in-house ultrasonic alignment rig containing a mixture of photocurable resin and discontinuous 14 μm diameter glass fibre reinforcement(50 μm length). In our study, a suitable print speed of 20 mm s-1 was used, which is comparable to conventional additive layer techniques. We show the ability to construct in-plane orthogonally aligned sections printed side by side, where the precise orientation of the configurations is controlled by switching the ultrasonic standing wave profile mid-print. This approach permits the realisation of complex fibrous architectures within a 3D printed landscape. The versatile nature of the ultrasonic manipulation technique also permits a wide range of particle types (diameters, aspect ratios and functions) and architectures (in-plane, and out-plane) to be patterned, leading to the creation of a new generation of fibrous reinforced composites for 3D printing.

  11. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

    Cao, Z.; Shi, J. J.; Torah, R. N.; Tudor, M. J.; Beeby, S. P.

    2015-12-01

    This work presents a vertically fabricated 3D thermoelectric generator (TEG) by dispenser printing on flexible polyimide substrate. This direct-write technology only involves printing of electrodes, thermoelectric active materials and structure material, which needs no masks to transfer the patterns onto the substrate. The dimension for single thermoelectric element is 2 mm × 2 mm × 0.5 mm while the distance between adjacent cubes is 1.2 mm. The polymer structure layer was used to support the electrodes which are printed to connect the top ends of the thermoelectric material and ensure the flexibility as well. The advantages and the limitations of the dispenser printed 3D TEGs will also be evaluated in this paper. The proposed method is potential to be a low-cost and scalable fabrication solution for TEGs.

  12. The 3-D inelastic analyses for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Hopkins, D. A.; Chamis, C. C.

    1989-01-01

    The 3-D inelastic analysis method is a focused program with the objective to develop computationally effective analysis methods and attendant computer codes for three-dimensional, nonlinear time and temperature dependent problems present in the hot section of turbojet engine structures. Development of these methods was a major part of the Hot Section Technology (HOST) program over the past five years at Lewis Research Center.

  13. 3D reconstruction methods of coronal structures by radio observations

    NASA Astrophysics Data System (ADS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-11-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  14. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

    Aschwanden, Markus J.; Bastian, T. S.; White, Stephen M.

    1992-01-01

    The ability to carry out the three dimensional (3D) reconstruction of structures in the solar corona would represent a major advance in the study of the physical properties in active regions and in flares. Methods which allow a geometric reconstruction of quasistationary coronal structures (for example active region loops) or dynamic structures (for example flaring loops) are described: stereoscopy of multi-day imaging observations by the VLA (Very Large Array); tomography of optically thin emission (in radio or soft x-rays); multifrequency band imaging by the VLA; and tracing of magnetic field lines by propagating electron beams.

  15. Observed Human Errors in Interpreting 3D visualizations: implications for Teaching Students how to Comprehend Geological Block Diagrams

    NASA Astrophysics Data System (ADS)

    Bemis, K. G.; Pirl, E.; Chiang, J.; Tremaine, M.

    2009-12-01

    Block diagrams are commonly used to communicate three dimensional geological structures and other phenomena relevant to geological science (e.g., water bodies in the ocean). However, several recent studies have suggested that these 3D visualizations create difficulties for individuals with low to moderate spatial abilities. We have therefore initiated a series of studies to understand what it is about the 3D structures that make them so difficult for some people and also to determine if we can improve people’s understanding of these structures through web-based training not related to geology or other underlying information. Our first study examined what mistakes subjects made in a set of 3D block diagrams designed to represent progressively more difficult internal structures. Each block was shown bisected by a plane either perpendicular or at an angle to the block sides. Five low to medium spatial subjects were asked to draw the features that would appear on the bisecting plane. They were asked to talk aloud as they solved the problem. Each session was videotaped. Using the time it took subjects to solve the problems, the subject verbalizations of their problem solving and the drawings that were found to be in error, we have been able to find common patterns in the difficulties the subjects had with the diagrams. We have used these patterns to generate a set of strategies the subjects used in solving the problems. From these strategies, we are developing methods of teaching. A problem found in earlier work on geology structures was not observed in our study, that is, one of subjects failing to recognize the 2D representation of the block as 3D and drawing the cross-section as a combined version of the visible faces of the object. We attribute this to our experiment introduction, suggesting that even this simple training needs to be carried out with students encountering 3D block diagrams. Other problems subjects had included difficulties in perceptually

  16. Application of Cutting-Edge 3D Seismic Attribute Technology to the Assessment of Geological Reservoirs for CO2 Sequestration

    SciTech Connect

    Christopher Liner; Jianjun Zeng; Po Geng Heather King Jintan Li; Jennifer Califf; John Seales

    2010-03-31

    The goals of this project were to develop innovative 3D seismic attribute technologies and workflows to assess the structural integrity and heterogeneity of subsurface reservoirs with potential for CO{sub 2} sequestration. Our specific objectives were to apply advanced seismic attributes to aide in quantifying reservoir properies and lateral continuity of CO{sub 2} sequestration targets. Our study area is the Dickman field in Ness County, Kansas, a type locality for the geology that will be encountered for CO{sub 2} sequestration projects from northern Oklahoma across the U.S. midcontent to Indiana and beyond. Since its discovery in 1962, the Dickman Field has produced about 1.7 million barrels of oil from porous Mississippian carbonates with a small structural closure at about 4400 ft drilling depth. Project data includes 3.3 square miles of 3D seismic data, 142 wells, with log, some core, and oil/water production data available. Only two wells penetrate the deep saline aquifer. Geological and seismic data were integrated to create a geological property model and a flow simulation grid. We systematically tested over a dozen seismic attributes, finding that curvature, SPICE, and ANT were particularly useful for mapping discontinuities in the data that likely indicated fracture trends. Our simulation results in the deep saline aquifer indicate two effective ways of reducing free CO{sub 2}: (a) injecting CO{sub 2} with brine water, and (b) horizontal well injection. A tuned combination of these methods can reduce the amount of free CO{sub 2} in the aquifer from over 50% to less than 10%.

  17. Dynactin 3D structure: implications for assembly and dynein binding.

    PubMed

    Imai, Hiroshi; Narita, Akihiro; Maéda, Yuichiro; Schroer, Trina A

    2014-09-23

    The multisubunit protein complex, dynactin, is an essential component of the cytoplasmic dynein motor. High-resolution structural work on dynactin and the dynein/dynactin supercomplex has been limited to small subunits and recombinant fragments that do not report fully on either ≈1MDa assembly. In the present study, we used negative-stain electron microscopy and image analysis based on random conical tilt reconstruction to obtain a three-dimensional (3D) structure of native vertebrate dynactin. The 35-nm-long dynactin molecule has a V-shaped shoulder at one end and a flattened tip at the other end, both offset relative to the long axis of the actin-related protein (Arp) backbone. The shoulder projects dramatically away from the Arp filament core in a way that cannot be appreciated in two-dimensional images, which has implications for the mechanism of dynein binding. The 3D structure allows the helical parameters of the entire Arp filament core, which includes the actin capping protein, CP, to be determined for the first time. This structure exhibits near identity to F-actin and can be well fitted into the dynactin envelope. Molecular fitting of modeled CP-Arp polymers into the envelope shows that the filament contains between 7 and 9 Arp protomers and is capped at both ends. In the 7 Arp model, which agrees best with measured Arp stoichiometry and other structural information, actin capping protein (CP) is not present at the distal tip of the structure, unlike what is seen in the other models. The 3D structure suggests a mechanism for dynactin assembly and length specification. PMID:25046383

  18. The deep geothermal potential of Berlin (Germany) - Predictions from 3D structural and thermal modelling

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Fuchs, Sven; Cacace, Mauro; Kastner, Oliver; Huenges, Ernst; Scheck-Wenderoth, Magdalena

    2013-04-01

    In the light of an aspired reduction of CO2 emissions for Germany's capital Berlin, one possible alternative for meeting the city's growing energy demands lies in deep geothermal energy. To minimise exploration risks, a profound knowledge about the subsurface temperature distribution is indispensable. We present a 3D structural model that is used for thermal modelling and thus correlates calculated subsurface temperatures with geothermally relevant structures in the deep subsurface of Berlin - an ideal base for improving the probability of finding adequate geothermal reservoirs. Berlin is located in the eastern part of the North German Basin which is filled with several thousand metres of Permian to Cenozoic sediments containing hot and water bearing aquifers to potentially be used as hydrothermal reservoirs. To characterise the geological underground, the 3D structural model integrates stratigraphical, petrophysical and well-log based information from local boreholes as well as stratigraphic trends from (seismic data based) regional 3D models. The model differentiates 21 geological units: 17 Permian-Cenozoic sedimentary layers, pre-Permian sediments, upper crust, lower crust and the lithospheric mantle. Based on this 3D geological model complemented by databased lithology-dependent thermal properties, two groups of numerical thermal simulations have been carried out: calculations of the steady-state conductive thermal field and simulations of coupled fluid and heat transport. The 3D thermal models predict large lateral variations in temperatures that are validated by high-precession temperature logs. These variations are mostly caused by three specific geological layers and their physical properties: the Permian Zechstein salt with its markedly high thermal conductivity and strong thickness variation (171-3442 m); the crystalline upper crustal layer with its high radiogenic heat production and decreasing thickness from east to west; and the Tertiary Rupelian

  19. 3D precision surface measurement by dynamic structured light

    NASA Astrophysics Data System (ADS)

    Franke, Ernest A.; Magee, Michael J.; Mitchell, Joseph N.; Rigney, Michael P.

    2004-02-01

    This paper describes a 3-D imaging technique developed as an internal research project at Southwest Research Institute. The technique is based on an extension of structured light methods in which a projected pattern of parallel lines is rotated over the surface to be measured. A sequence of images is captured and the surface elevation at any location can then be determined from measurements of the temporal pattern, at any point, without considering any other points on the surface. The paper describes techniques for system calibration and surface measurement based on the method of projected quadric shells. Algorithms were developed for image and signal analysis and computer programs were written to calibrate the system and to calculate 3-D coordinates of points on a measured surface. A prototype of the Dynamic Structured Light (DSL) 3-D imaging system was assembled and typical parts were measured. The design procedure was verified and used to implement several different configurations with different measurement volumes and measurement accuracy. A small-parts measurement accuracy of 32 micrometers (.0012") RMS was verified by measuring the surface of a precision-machined plane. Large aircraft control surfaces were measured with a prototype setup that provided .02" depth resolution over a 4" by 8" field of view. Measurement times are typically less than three minutes for 300,000 points. A patent application has been filed.

  20. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  1. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

    Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

    2012-07-01

    In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

  2. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

    There are far fewer classes of three-dimensional protein folds than sequence families but the problem of detecting three-dimensional similarities is NP-complete. We present a novel heuristic for identifying 3-D similarities between a query structure and the database of known protein structures. Many methods for structure alignment use a bottom-up approach, identifying first local matches and then solving a combinatorial problem in building up larger clusters of matching substructures. Here the top-down approach is to start with the global comparison and select a rough superimposition using a fast 3-D lookup of secondary structure motifs. The superimposition is then extended to an alignment of C{sup {alpha}} atoms by an iterative dynamic programming step. An all-against-all comparison of 385-representative proteins (150,000 pair comparisons) took 1 day of computer time on a single R8000 processor. In other words, one query structure is scanned against the database in a matter of minutes. The method is rated at 90% reliability at capturing statistically significant similarities. It is useful as a rapid preprocessor to a comprehensive protein structure database search system.

  3. Integrating 3D geological information with a national physically-based hydrological modelling system

    NASA Astrophysics Data System (ADS)

    Lewis, Elizabeth; Parkin, Geoff; Kessler, Holger; Whiteman, Mark

    2016-04-01

    Robust numerical models are an essential tool for informing flood and water management and policy around the world. Physically-based hydrological models have traditionally not been used for such applications due to prohibitively large data, time and computational resource requirements. Given recent advances in computing power and data availability, a robust, physically-based hydrological modelling system for Great Britain using the SHETRAN model and national datasets has been created. Such a model has several advantages over less complex systems. Firstly, compared with conceptual models, a national physically-based model is more readily applicable to ungauged catchments, in which hydrological predictions are also required. Secondly, the results of a physically-based system may be more robust under changing conditions such as climate and land cover, as physical processes and relationships are explicitly accounted for. Finally, a fully integrated surface and subsurface model such as SHETRAN offers a wider range of applications compared with simpler schemes, such as assessments of groundwater resources, sediment and nutrient transport and flooding from multiple sources. As such, SHETRAN provides a robust means of simulating numerous terrestrial system processes which will add physical realism when coupled to the JULES land surface model. 306 catchments spanning Great Britain have been modelled using this system. The standard configuration of this system performs satisfactorily (NSE > 0.5) for 72% of catchments and well (NSE > 0.7) for 48%. Many of the remaining 28% of catchments that performed relatively poorly (NSE < 0.5) are located in the chalk in the south east of England. As such, the British Geological Survey 3D geology model for Great Britain (GB3D) has been incorporated, for the first time in any hydrological model, to pave the way for improvements to be made to simulations of catchments with important groundwater regimes. This coupling has involved

  4. Interpretation and mapping of geological features using mobile devices for 3D outcrop modelling

    NASA Astrophysics Data System (ADS)

    Buckley, Simon J.; Kehl, Christian; Mullins, James R.; Howell, John A.

    2016-04-01

    Advances in 3D digital geometric characterisation have resulted in widespread adoption in recent years, with photorealistic models utilised for interpretation, quantitative and qualitative analysis, as well as education, in an increasingly diverse range of geoscience applications. Topographic models created using lidar and photogrammetry, optionally combined with imagery from sensors such as hyperspectral and thermal cameras, are now becoming commonplace in geoscientific research. Mobile devices (tablets and smartphones) are maturing rapidly to become powerful field computers capable of displaying and interpreting 3D models directly in the field. With increasingly high-quality digital image capture, combined with on-board sensor pose estimation, mobile devices are, in addition, a source of primary data, which can be employed to enhance existing geological models. Adding supplementary image textures and 2D annotations to photorealistic models is therefore a desirable next step to complement conventional field geoscience. This contribution reports on research into field-based interpretation and conceptual sketching on images and photorealistic models on mobile devices, motivated by the desire to utilise digital outcrop models to generate high quality training images (TIs) for multipoint statistics (MPS) property modelling. Representative training images define sedimentological concepts and spatial relationships between elements in the system, which are subsequently modelled using artificial learning to populate geocellular models. Photorealistic outcrop models are underused sources of quantitative and qualitative information for generating TIs, explored further in this research by linking field and office workflows through the mobile device. Existing textured models are loaded to the mobile device, allowing rendering in a 3D environment. Because interpretation in 2D is more familiar and comfortable for users, the developed application allows new images to be captured

  5. Structure and magnetic exchange in heterometallic 3d-3d transition metal triethanolamine clusters.

    PubMed

    Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S

    2012-01-21

    Synthetic methods are described that have resulted in the formation of seven heterometallic complexes, all of which contain partially deprotonated forms of the ligand triethanolamine (teaH(3)). These compounds are [Mn(III)(4)Co(III)(2)Co(II)(2)O(2)(teaH(2))(2)(teaH)(0.82)(dea)(3.18)(O(2)CMe)(2)(OMe)(2)](BF(4))(2)(O(2)CMe)(2)·3.18MeOH·H(2)O (1), [Mn(II)(2)Mn(III)(2)Co(III)(2)(teaH)(4)(OMe)(2)(acac)(4)](NO(3))(2)·2MeOH (2), [Mn(III)(2)Ni(II)(4)(teaH)(4)(O(2)CMe)(6)]·2MeCN (3), [Mn(III)(2)Co(II)(2)(teaH)(2)(sal)(2)(acac)(2)(MeOH)(2)]·2MeOH (4), [Mn(II)(2)Fe(III)(2)(teaH)(2)(paa)(4)](NO(3))(2)·2MeOH·CH(2)Cl(2) (5), [Mn(II)Mn(III)(2)Co(III)(2)O(teaH)(2)(dea)(Iso)(OMe)(F)(2)(Phen)(2)](BF(4))(NO(3))·3MeOH (6) and [Mn(II)(2)Mn(III)Co(III)(2)(OH)(teaH)(3)(teaH(2))(acac)(3)](NO(3))(2)·3CH(2)Cl(2) (7). All of the compounds contain manganese, combined with 3d transition metal ions such as Fe, Co and Ni. The crystal structures are described and examples of 'rods', tetranuclear 'butterfly' and 'triangular' Mn(3) cluster motifs, flanked in some cases by diamagnetic cobalt(III) centres, are presented. Detailed DC and AC magnetic susceptibility and magnetization studies, combined with spin Hamiltonian analysis, have yielded J values and identified the spin ground states. In most cases, the energies of the low-lying excited states have also been obtained. The features of note include the 'inverse butterfly' spin arrangement in 2, 4 and 5. A S = 5/2 ground state occurs, for the first time, in the Mn(III)(2)Mn(II) triangular moiety within 6, the many other reported [Mn(3)O](6+) examples having S = ½ or 3/2 ground states. Compound 7 provides the first example of a Mn(II)(2)Mn(III) triangle, here within a pentanuclear Mn(3)Co(2) cluster. PMID:22113523

  6. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    PubMed Central

    Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2013-01-01

    Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution afforded by live-cell microscopy is limited (~ 200 nm). Our work was aimed at developing a correlation method that permits direct visualization of early events of HIV-1 infection by combining live-cell fluorescent light microscopy, cryo-fluorescent microscopy, and cryoET. In this manner, live-cell and cryo-fluorescent signals can be used to accurately guide the sampling in cryoET. Furthermore, structural information obtained from cryoET can be complemented with the dynamic functional data gained through live-cell imaging of fluorescent labeled target. In this video article, we provide detailed methods and protocols for structural investigation of HIV-1 and host-cell interactions using 3D correlative high-speed live-cell imaging and high-resolution cryoET structural analysis. HeLa cells infected with HIV-1 particles were characterized first by confocal live-cell microscopy, and the region containing the same viral particle was then analyzed by cryo-electron tomography for 3D structural details. The correlation between two sets of imaging data, optical imaging and electron imaging, was achieved using a home-built cryo-fluorescence light microscopy stage. The approach detailed here will be valuable, not only for study of virus-host cell interactions, but also for broader applications in cell biology, such as cell signaling, membrane receptor trafficking, and many other dynamic cellular processes. PMID:23852318

  7. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

    A new image matching technique is described. It is implemented as an object-independent hierarchical structural juxtaposition algorithm based on an alphabet of simple object-independent contour structural elements. The structural matching applied implements an optimized method of walking through a truncated tree of all possible juxtapositions of two sets of structural elements. The algorithm was initially developed for dealing with 2D images such as the aerospace photographs, and it turned out to be sufficiently robust and reliable for matching successfully the pictures of natural landscapes taken in differing seasons from differing aspect angles by differing sensors (the visible optical, IR, and SAR pictures, as well as the depth maps and geographical vector-type maps). At present (in the reported version), the algorithm is enhanced based on additional use of information on third spatial coordinates of observed points of object surfaces. Thus, it is now capable of matching the images of 3D scenes in the tasks of automatic navigation of extremely low flying unmanned vehicles or autonomous terrestrial robots. The basic principles of 3D structural description and matching of images are described, and the examples of image matching are presented.

  8. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  9. 3D Seismic Characterization of the Research Facility for Geological Storage of CO2: Hontomín (Burgos, Spain)

    NASA Astrophysics Data System (ADS)

    Alcalde, J.; Martí, D.; Calahorrano, A.; Marzan, I.; Ayarza, P.; Carbonell, R.; Perez-Estaun, A.

    2011-12-01

    A technological research facility dedicated to the underground geological storage of CO2 is currently being developed by the Spanish research program on Carbon Capture and Storage (CCS) in Hontomin (Burgos, North of the Iberian Peninsula) This research program is being developed by the CIUDEN Foundation. CIUDEN is an initiative of 3 Spanish state departments (Science & Innovation, Environment and Industry). An extensive multidisciplinary site characterization phase has been carried out, including a multi-seismic data acquisition experiment. Within this effort a 36 km2 academic-oriented 3D seismic reflection survey was acquired in summer 2010. The aim of data acquisition effort are to provide high resolution images of the subsurface of the storage complex, constrain a baseline model for all the disciplines involved in the project. The main acquisition characteristics of this survey included: a mixed source (Vibroseis & explosive , 74% and 26% of the source points, respectively); 5000 shot points, distributed along 22 source lines (separated 250 m), 22 lines of receivers (separated 275 m); shot and receiver spacing along the source and receiver lines was of 25 m; this resulted in a nominal CDP-fold of 36 traces, with 13 m2 bins. This 3D-data was fully processed until migration. The main features within the processing sequence include static correction calculation, frequency filtering, trace amplitude equalization, rms velocity modeling, FK-domain filtering, 3D deconvolution, dip move-out corrections, residual static calculation and pre and post stack migration. The final high-resolution 3D-volume allowed to characterize the main tectonic structure of the dome complex, the fault system of the area and the feasibility of the reservoir for the storage. The target reservoir is a saline aquifer placed at 1400, approximately, within Lower Jurassic carbonates (Lias); the main seal is formed by inter-layered marls and marly limestones from Early to Middle Jurassic (Dogger

  10. Engineering extracellular matrix structure in 3D multiphase tissues

    PubMed Central

    Gillette, Brian M.; Rossen, Ninna S.; Das, Nikkan; Leong, Debra; Wang, Meixin; Dugar, Arushi; Sia, Samuel K.

    2011-01-01

    In native tissues, microscale variations in the extracellular matrix (ECM) structure can drive different cellular behaviors. Although control over ECM structure could prove useful in tissue engineering and in studies of cellular behavior, isotropic 3D matrices poorly replicate variations in local microenvironments. In this paper, we demonstrate a method to engineer local variations in the density and size of collagen fibers throughout 3D tissues. The results showed that, in engineered multiphase tissues, the structures of collagen fibers in both the bulk ECM phases (as measured by mesh size and width of fibers) as well as at tissue interfaces (as measured by density of fibers and thickness of tissue interfaces) could be modulated by varying the collagen concentrations and gelling temperatures. As the method makes use of a previously published technique for tissue bonding, we also confirmed that significant adhesion strength at tissue interfaces was achieved under all conditions tested. Hence, this study demonstrates how collagen fiber structures can be engineered within all regions of a tightly integrated multiphase tissue scaffold by exploiting knowledge of collagen assembly. PMID:21840047

  11. Construction of 3-D geologic framework and textural models for Cuyama Valley groundwater basin, California

    USGS Publications Warehouse

    Sweetkind, Donald S.; Faunt, Claudia C.; Hanson, Randall T.

    2013-01-01

    Groundwater is the sole source of water supply in Cuyama Valley, a rural agricultural area in Santa Barbara County, California, in the southeasternmost part of the Coast Ranges of California. Continued groundwater withdrawals and associated water-resource management concerns have prompted an evaluation of the hydrogeology and water availability for the Cuyama Valley groundwater basin by the U.S. Geological Survey, in cooperation with the Water Agency Division of the Santa Barbara County Department of Public Works. As a part of the overall groundwater evaluation, this report documents the construction of a digital three-dimensional geologic framework model of the groundwater basin suitable for use within a numerical hydrologic-flow model. The report also includes an analysis of the spatial variability of lithology and grain size, which forms the geologic basis for estimating aquifer hydraulic properties. The geologic framework was constructed as a digital representation of the interpreted geometry and thickness of the principal stratigraphic units within the Cuyama Valley groundwater basin, which include younger alluvium, older alluvium, and the Morales Formation, and underlying consolidated bedrock. The framework model was constructed by creating gridded surfaces representing the altitude of the top of each stratigraphic unit from various input data, including lithologic and electric logs from oil and gas wells and water wells, cross sections, and geologic maps. Sediment grain-size data were analyzed in both two and three dimensions to help define textural variations in the Cuyama Valley groundwater basin and identify areas with similar geologic materials that potentially have fairly uniform hydraulic properties. Sediment grain size was used to construct three-dimensional textural models that employed simple interpolation between drill holes and two-dimensional textural models for each stratigraphic unit that incorporated spatial structure of the textural data.

  12. Complete Tem-Tomography: 3D Structure of Gems Cluster

    NASA Technical Reports Server (NTRS)

    Matsuno, J.; Miyake, A.; Tsuchiyama, A.; Messenger, S.; Nakamura-Messenger, K.

    2015-01-01

    GEMS (glass with embedded metal and sulfide) grains in interplanetary dust particles (IDPs) are considered to be one of the ubiquitous and fundamental building blocks of solids in the Solar System. They have been considered to be interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk but the elemental and isotopic composition measurements suggest that most of them have been formed in the protoplanetary disk as condensates from high temperature gas. This formation model is also supported by the formation of GEMS-like grains with respect to the size, mineral assemblage, texture and infrared spectrum by condensation experiments from mean GEMS composition materials. Previous GEMS studies were performed only with 2D observation by transmission electron microscopy (TEM) or scanning TEM (STEM). However, the 3D shape and structure of GEMS grains and the spatial distribution of Fe/FeS's has critical information about their formation and origin. Recently, the 3D structure of GEMS grains in ultrathin sections of cluster IDPs was revealed by electron tomography using a TEM/STEM (JEM-2100F, JEOL). However, CT images of thin sections mounted on Cu grids acquired by conventional TEM-tomography are limited to low tilt angles (e. g., less than absolute value of 75 deg. In fact, previous 3D TEM observations of GEMS were affected by some artifacts related to the limited tilt range in the TEM used. Complete tomographic images should be acquired by rotating the sample tilt angle over a range of more than absolute value of 80 deg otherwise the CT images lose their correct structures. In order to constrain the origin and formation process of GEMS grains more clearly, we performed complete electron tomography for GEMS grains. Here we report the sample preparation method we have developed for this study, and the preliminary results.

  13. High resolution 3D ERT to help GPR data interpretation for researching archaeological items in a geologically complex subsurface

    NASA Astrophysics Data System (ADS)

    Negri, S.; Leucci, G.; Mazzone, F.

    2008-09-01

    Muro Leccese (Lecce) contains one the most important Messapian archaeological sites in southern Italy. The archaeological interest of the site arises from the discovery of the remains of Messapian walls, tombs, roads, etc. (4th-2nd centuries BC) in the neighbourhood. The archaeological remains were found at about 0.3 m depth. At present the site belongs to the municipality, which intends to build a new sewer network through it. The risk of destroying potentially interesting ancient archaeological structures during the works prompted an archaeological survey of the area. The relatively large dimensions of the area (almost 10,000 m 2), together with time and cost constraints, made it necessary to use geophysical investigations as a faster means to ascertain the presence of archaeological items. Since the most important targets were expected to be located at a soil depth of about 0.3 m, a ground-penetrating radar (GPR) survey was carried out in an area located near the archaeological excavations. Unfortunately the geological complexity did not allow an easy interpretation of the GPR data. Therefore a 3D electrical resistivity tomography (ERT) scan was conducted in order to resolve these interpretation problems. A three-way comparison of the results of the dense ERT measurements parallel to the x axis, the results of the measurements parallel to the y axis and the combined results was performed. Subsequently the synthetic model approach was used to provide a better characterization of the resistivity anomalies visible on the ERT field data. The 3D inversion results clearly illustrate the capability to resolve in view of quality 3D structures of archaeological interest. According to the presented data the inversion models along one direction ( x or y) seems to be adequate in reconstructing the subsurface structures. Naturally field data produce good quality reconstructions of the archaeological features only if the x-line and y-line measurements are considered together

  14. Geological and paleogeographic implications of late Cretaceous pockmarks: a 3D seismic study onshore South Denmark

    NASA Astrophysics Data System (ADS)

    Clausen, Ole R.; Andresen, Katrine J.; Lisager, Peter

    2015-04-01

    The objective of this presentation is to introduce hereto not described elongated pockmarks observed at an intra-Chalk Group (Late Cretaceous) surface and to present the geological and paleogeographic significance of the observations. The study utilizes an onshore 3D seismic survey, located at the southern flank of the Ringkøbing-Fyn High (RFH) at the Sundeved peninsular in southern Denmark to perform the detailed analysis of the Chalk Group in the area. The top of the Chalk Group, which do not feature any pockmarks, is located at 200-400mbsl and dips smoothly towards the SSW. It is offset by arrays of normal faults, which detach at the top of the Zechstein. The Chalk Group in the study area shows two distinct seismic facies. A lower facies with relatively high intensity coherent reflections and an upper facies with much less pronounced and diffuse internal reflectivity. The surface separating the two facies, features abundant circular (c. 0.3km wide) to elongated (0.3km x 2km) NW-SE striking depressions, which we interpret as pockmarks. The N-S striking faults in the study area offset the elongate pockmarks and thus clearly post-date the pockmark formation. However, the E-W striking faults appear to have formed at the same time as the pockmarks which adjacent and parallel to the E-W striking faults are mainly circular and only observed in the hangingwall block. No significant faulting or other evidence of vertical migration routes directly beneath the pockmarks has been observed. Borehole information, however, indicates a slightly increased clay-content in the sediments filling the pockmarks, as well as an increase in seismic velocity at the pockmarked surface indicative of hard ground development. Thus fluid expulsion and initial pockmark formation apparently coincided with a period of ceased sedimentation. The pockmarks were later excavated by submarine currents controlled by the orientation of the underlying RFH, very similar to elongated pockmarks reported in

  15. Algorithms for extraction of structural attitudes from 3D outcrop models

    NASA Astrophysics Data System (ADS)

    Duelis Viana, Camila; Endlein, Arthur; Ademar da Cruz Campanha, Ginaldo; Henrique Grohmann, Carlos

    2016-05-01

    The acquisition of geological attitudes on rock cuts using traditional field compass survey can be a time consuming, dangerous, or even impossible task depending on the conditions and location of outcrops. The importance of this type of data in rock-mass classifications and structural geology has led to the development of new techniques, in which the application of photogrammetric 3D digital models has had an increasing use. In this paper we present two algorithms for extraction of attitudes of geological discontinuities from virtual outcrop models: ply2atti and scanline, implemented with the Python programming language. The ply2atti algorithm allows for the virtual sampling of planar discontinuities appearing on the 3D model as individual exposed surfaces, while the scanline algorithm allows the sampling of discontinuities (surfaces and traces) along a virtual scanline. Application to digital models of a simplified test setup and a rock cut demonstrated a good correlation between the surveys undertaken using traditional field compass reading and virtual sampling on 3D digital models.

  16. 1-D/3-D geologic model of the Western Canada Sedimentary Basin

    USGS Publications Warehouse

    Higley, D.K.; Henry, M.; Roberts, L.N.R.; Steinshouer, D.W.

    2005-01-01

    The 3-D geologic model of the Western Canada Sedimentary Basin comprises 18 stacked intervals from the base of the Devonian Woodbend Group and age equivalent formations to ground surface; it includes an estimated thickness of eroded sediments based on 1-D burial history reconstructions for 33 wells across the study area. Each interval for the construction of the 3-D model was chosen on the basis of whether it is primarily composed of petroleum system elements of reservoir, hydrocarbon source, seal, overburden, or underburden strata, as well as the quality and areal distribution of well and other data. Preliminary results of the modeling support the following interpretations. Long-distance migration of hydrocarbons east of the Rocky Mountains is indicated by oil and gas accumulations in areas within which source rocks are thermally immature for oil and (or) gas. Petroleum systems in the basin are segmented by the northeast-trending Sweetgrass Arch; hydrocarbons west of the arch were from source rocks lying near or beneath the Rocky Mountains, whereas oil and gas east of the arch were sourced from the Williston Basin. Hydrocarbon generation and migration are primarily due to increased burial associated with the Laramide Orogeny. Hydrocarbon sources and migration were also influenced by the Lower Cretaceous sub-Mannville unconformity. In the Peace River Arch area of northern Alberta, Jurassic and older formations exhibit high-angle truncations against the unconformity. Potential Paleozoic though Mesozoic hydrocarbon source rocks are in contact with overlying Mannville Group reservoir facies. In contrast, in Saskatchewan and southern Alberta the contacts are parallel to sub-parallel, with the result that hydrocarbon source rocks are separated from the Mannville Group by seal-forming strata within the Jurassic. Vertical and lateral movement of hydrocarbons along the faults in the Rocky Mountains deformed belt probably also resulted in mixing of oil and gas from numerous

  17. 3D geological to geophysical modelling and seismic wave propagation simulation: a case study from the Lalor Lake VMS (Volcanogenic Massive Sulphides) mining camp

    NASA Astrophysics Data System (ADS)

    Miah, Khalid; Bellefleur, Gilles

    2014-05-01

    The global demand for base metals, uranium and precious metals has been pushing mineral explorations at greater depth. Seismic techniques and surveys have become essential in finding and extracting mineral rich ore bodies, especially for deep VMS mining camps. Geophysical parameters collected from borehole logs and laboratory measurements of core samples provide preliminary information about the nature and type of subsurface lithologic units. Alteration halos formed during the hydrothermal alteration process contain ore bodies, which are of primary interests among geologists and mining industries. It is known that the alteration halos are easier to detect than the ore bodies itself. Many 3D geological models are merely projection of 2D surface geology based on outcrop inspections and geochemical analysis of a small number of core samples collected from the area. Since a large scale 3D multicomponent seismic survey can be prohibitively expensive, performance analysis of such geological models can be helpful in reducing exploration costs. In this abstract, we discussed challenges and constraints encountered in geophysical modelling of ore bodies and surrounding geologic structures from the available coarse 3D geological models of the Lalor Lake mining camp, located in northern Manitoba, Canada. Ore bodies in the Lalor lake VMS camp are rich in gold, zinc, lead and copper, and have an approximate weight of 27 Mt. For better understanding of physical parameters of these known ore bodies and potentially unknown ones at greater depth, we constructed a fine resolution 3D seismic model with dimensions: 2000 m (width), 2000 m (height), and 1500 m (vertical depth). Seismic properties (P-wave, S-wave velocities, and density) were assigned based on a previous rock properties study of the same mining camp. 3D finite-difference elastic wave propagation simulation was performed in the model using appropriate parameters. The generated synthetic 3D seismic data was then compared to

  18. Characterizing 3D Vegetation Structure from Space: Mission Requirements

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G.; Bergen, Kathleen; Blair, James B.; Dubayah, Ralph; Houghton, Richard; Hurtt, George; Kellndorfer, Josef; Lefsky, Michael; Ranson, Jon; Saatchi, Sasan; Shugart, H. H.; Wickland, Diane

    2012-01-01

    Human and natural forces are rapidly modifying the global distribution and structure of terrestrial ecosystems on which all of life depends, altering the global carbon cycle, affecting our climate now and for the foreseeable future, causing steep reductions in species diversity, and endangering Earth s sustainability. To understand changes and trends in terrestrial ecosystems and their functioning as carbon sources and sinks, and to characterize the impact of their changes on climate, habitat and biodiversity, new space assets are urgently needed to produce high spatial resolution global maps of the three-dimensional (3D) structure of vegetation, its biomass above ground, the carbon stored within and the implications for atmospheric green house gas concentrations and climate. These needs were articulated in a 2007 National Research Council (NRC) report (NRC, 2007) recommending a new satellite mission, DESDynI, carrying an L-band Polarized Synthetic Aperture Radar (Pol-SAR) and a multi-beam lidar (Light RAnging And Detection) operating at 1064 nm. The objectives of this paper are to articulate the importance of these new, multi-year, 3D vegetation structure and biomass measurements, to briefly review the feasibility of radar and lidar remote sensing technology to meet these requirements, to define the data products and measurement requirements, and to consider implications of mission durations. The paper addresses these objectives by synthesizing research results and other input from a broad community of terrestrial ecology, carbon cycle, and remote sensing scientists and working groups. We conclude that: (1) current global biomass and 3-D vegetation structure information is unsuitable for both science and management and policy. The only existing global datasets of biomass are approximations based on combining land cover type and representative carbon values, instead of measurements of actual biomass. Current measurement attempts based on radar and multispectral

  19. Assessing quality of urban underground spaces by coupling 3D geological models: The case study of Foshan city, South China

    NASA Astrophysics Data System (ADS)

    Hou, Weisheng; Yang, Liang; Deng, Dongcheng; Ye, Jing; Clarke, Keith; Yang, Zhijun; Zhuang, Wenming; Liu, Jianxiong; Huang, Jichun

    2016-04-01

    Urban underground spaces (UUS), especially those containing natural resources that have not yet been utilized, have been recognized as important for future sustainable development in large cities. One of the key steps in city planning is to estimate the quality of urban underground space resources, since they are major determinants of suitable land use. Yet geological constraints are rarely taken into consideration in urban planning, nor are the uncertainties in the quality of the available assessments. Based on Fuzzy Set theory and the analytic hierarchy process, a 3D stepwise process for the quality assessment of geotechnical properties of natural resources in UUS is presented. The process includes an index system for construction factors; area partitioning; the extraction of geological attributes; the creation of a relative membership grade matrix; the evaluation of subject and destination layers; and indeterminacy analysis. A 3D geological model of the study area was introduced into the process that extracted geological attributes as constraints. This 3D geological model was coupled with borehole data for Foshan City, Guangdong province, South China, and the indeterminacies caused by the cell size and the geological strata constraints were analyzed. The results of the case study show that (1) a relatively correct result can be obtained if the cell size is near to the average sampling distance of the boreholes; (2) the constraints of the 3D geological model have a major role in establishing the UUS quality level and distribution, especially at the boundaries of the geological bodies; and (3) the assessment result is impacted by an interaction between the cell resolution and the geological model used.

  20. Structural analysis of tropical cyclone using INSAT-3D observations

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

    The continuous observations from visible and thermal infrared (TIR) channels of geostationary satellites are highly useful for obtaining the features associated with the shape and dynamics of cloud structures within the tropical cyclones (TCs). As TC develops from an unstructured cloud cluster and intensifies, the cloud structures become more axisymmetric around the centre of the TC. To better understand the structure of TC during different stages of its evolution i.e. from its cyclogenesis to maturity and dissipation, the continuous satellite observations plays a key role. The high spatial and temporal resolution observations from geostationary satellites are very useful in order to analyze the cloud organization during the cyclogenesis. The gradient of the brightness temperatures measures the level of symmetry of each structure, which characterizes the degree of cloud organization of the TC. In the present work, the structural analysis of TC during its life period using the observations from Indian geostationary satellite INSAT-3D has been discussed. The visible and TIR observations from INSAT-3D satellite were used to fix the center position of the cyclone which is an input for the cyclone track and intensity prediction models. This data is also used to estimate the intensity of cyclone in the advanced Dvorak technique (ADT), and in the estimation of radius of maximum winds (Rmax) of TC which is an essential input parameter for the prediction of storm surge associated to the cyclones. The different patterns of cloud structure during the intensification stage, eye-wall formation and dissipation have been discussed. The early identification of these features helps in predicting the rapid intensification of TC which in turn improves the intensity predictions.

  1. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

    Sheridan, Robert; Hopf, Thomas A.; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing. In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy. We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues., including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7–4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein

  2. Innovative 3D and 4D geological interpretation, modelling and visualisation techniques for subsurface characterisation of complex industrial sites - examples in the UK nuclear industry

    NASA Astrophysics Data System (ADS)

    Smith, Nicholas; Shevelan, John; Hodgetts, David; Head, William

    2013-04-01

    structural information. Detailed examination of these alongside numerous borehole logs and existing and new low-resolution geophysical data has allowed the creation of 3D geological interpretations and models, enabling the construction of 3D and 4D hydrogeological and contaminant transport models that are essential to environmental safety cases. Staying within the nuclear industry, geological characterisation issues may become even more prevalent in the UK's search for a location to build a geological disposal facility (GDF) for the disposal of its higher resolution radioactive waste. Here intrusive investigations would typically involve the drilling of boreholes, yet intrusion needs to be kept to a minimum. However, we show how innovative laser-based digital data gathering techniques which are currently being employed in the development of 3D structural models of crystalline rocks, are likely to be vital to the geological characterisation of the deep subsurface at potential UK locations for a GDF whilst keeping intrusion to a minimum.

  3. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

    Clancy, Neil T.; Lin, Jianyu; Arya, Shobhit; Hanna, George B.; Elson, Daniel S.

    2015-03-01

    Intraoperative feedback on tissue function, such as blood volume and oxygenation would be useful to the surgeon in cases where current clinical practice relies on subjective measures, such as identification of ischaemic bowel or tissue viability during anastomosis formation. Also, tissue surface profiling may be used to detect and identify certain pathologies, as well as diagnosing aspects of tissue health such as gut motility. In this paper a dual modality laparoscopic system is presented that combines multispectral reflectance and 3D surface imaging. White light illumination from a xenon source is detected by a laparoscope-mounted fast filter wheel camera to assemble a multispectral image (MSI) cube. Surface shape is then calculated using a spectrally-encoded structured light (SL) pattern detected by the same camera and triangulated using an active stereo technique. Images of porcine small bowel were acquired during open surgery. Tissue reflectance spectra were acquired and blood volume was calculated at each spatial pixel across the bowel wall and mesentery. SL features were segmented and identified using a `normalised cut' algoritm and the colour vector of each spot. Using the 3D geometry defined by the camera coordinate system the multispectral data could be overlaid onto the surface mesh. Dual MSI and SL imaging has the potential to provide augmented views to the surgeon supplying diagnostic information related to blood supply health and organ function. Future work on this system will include filter optimisation to reduce noise in tissue optical property measurement, and minimise spot identification errors in the SL pattern.

  4. Forward and Reverse Modeling Compressive Deformation in a 3D Geologic Model along the Central San Andreas Fault Zone

    NASA Astrophysics Data System (ADS)

    Roberts, M. A.; Graymer, R. W.; McPhee, D.

    2015-12-01

    During the late Miocene, a small change in the relative motion of the Pacific plate resulted in compressive as well as translational deformation along the central San Andreas Fault (SAF), creating thrust faults and folds throughout this region of California. We constructed a 3D model of an upper crustal volume between Pinnacles National Park and Gold Hill by assembling geologic map data and cross sections, geophysical data, and petroleum well logs in MoveTm, software which has the ability to forward and reverse model movement along faults and folds. For this study, we chose a blind thrust fault west of the SAF near Parkfield to compare deformation produced by MoveTm's forward modeling algorithm with that observed. We chose various synclines east of the SAF to explore the software's ability to unfold (reverse model) units. For the initial round of modeling, strike-slip movement has been omitted as the fault algorithm was designed primarily for extensional or compressional environments. Preliminary forward modeling of originally undeformed strata along the blind thrust produced geometries similar to those in the present-day 3D geologic model. The modeled amount of folding produced in hanging wall strata was less severe, suggesting these units were slightly folded before displacement. Based on these results, the algorithm shows potential in predicting deformation related to blind thrusts. Contraction in the region varies with fold axis location and orientation. MoveTm's unfolding algorithm can allow researchers to measure the amount of contraction a fold represents, and compare that amount across the modeled area as a way of observing regional stress patterns. The unfolding algorithm also allows for passive deformation of strata unconformably underlying the fold; one example reveals a steeper orientation of Cretaceous units prior to late Miocene deformation. Such modeling capabilities can allow for a better understanding of the structural history of the region.

  5. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

    OToole, Matthew; Mather, John; Kutulakos, Kiriakos N

    2016-07-01

    We consider the problem of deliberately manipulating the direct and indirect light flowing through a time-varying, general scene in order to simplify its visual analysis. Our approach rests on a crucial link between stereo geometry and light transport: while direct light always obeys the epipolar geometry of a projector-camera pair, indirect light overwhelmingly does not. We show that it is possible to turn this observation into an imaging method that analyzes light transport in real time in the optical domain, prior to acquisition. This yields three key abilities that we demonstrate in an experimental camera prototype: (1) producing a live indirect-only video stream for any scene, regardless of geometric or photometric complexity; (2) capturing images that make existing structured-light shape recovery algorithms robust to indirect transport; and (3) turning them into one-shot methods for dynamic 3D shape capture. PMID:27295455

  6. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  7. Surface amplitude data: 3D-seismic for interpretation of sea floor geology (Louisiana Slope)

    SciTech Connect

    Roberts, H.H.

    1996-09-01

    Proliferation of 3D-seismic in support of hydrocarbon exploration/production has created new data for improved interpretation of sea floor and shallow subsurface geology. Processing of digital seismic data to enhance amplitude anomalies produces information for improved assessment of geohazards and identification of sensitive benthic communities protected by environmental regulations. Coupled with high resolution acoustic data and direct observation/sampling using a manned research submersible, surface amplitude maps add critical interpretive information for identification of sea floor features. Non-reflective zones (acoustic wipeouts) are associated with many slope features. Mud diapirs, mud mounds, mud volcanoes, gas-changed sediments, gas hydrates, slump deposits, carbonate hardgrounds, and various types of carbonate mounds are all features that exhibit this common response on high resolution seismic profiles. Amplitude data help make specific identifications. Since 1988, submersible data from mid-to-upper slope features (Garden Banks, Green Canyon, and Mississippi Canyon lease block areas) have been analyzed with conventional high resolution acoustic data and 313-amplitude extraction maps. Areas of rapid venting of sediment and hydrocarbon-charged formation fluids are clearly distinguishable from mud diapirs and areas of carbonate mounds (slow seepage). Gas hydrates occur as mounds and mounded zones along faults; products of moderate flux rates below (approx.) 500 in water depths. Gas hydrates function as stored trophic resources that support sensitive chemosynthetic communities. Amplitude extraction maps clearly identify these features by a strong low impedance amplitude anomaly. Refinement and {open_quotes}field calibration{close_quotes} of the surface amplitude extraction method may eventually lead to a new standard for evaluating geohazards and sensitive benthic communities.

  8. 3D Geologic Modeling of the Southern San Joaquin Basin for the Westcarb Kimberlina Demonstration Project- A Status Report

    SciTech Connect

    Wagoner, J

    2009-02-23

    The objective of the Westcarb Kimberlina pilot project is to safely inject 250,000 t CO{sub 2}/yr for four years into the deep subsurface at the Clean Energy Systems (CES) Kimberlina power plant in southern San Joaquin Valley, California. In support of this effort, we have constructed a regional 3D geologic model of the southern San Joaquin basin. The model is centered on the Kimberlina power plant and spans the UTM range E 260000-343829 m and N 3887700-4000309 m; the depth of the model ranges from the topographic surface to >9000 m below sea level. The mapped geologic units are Quaternary basin fill, Tertiary marine and continental deposits, and pre-Tertiary basement rocks. Detailed geologic data, including surface maps, borehole data, and geophysical surveys, were used to define the geologic framework. Fifteen time-stratigraphic formations were mapped, as well as >140 faults. The free surface is based on a 10 m lateral resolution DEM. We use Earthvision (Dynamic Graphics, Inc.) to integrate the geologic and geophysical information into a 3D model of x,y,z,p nodes, where p is a unique integer index value representing the geologic unit. This grid represents a realistic model of the subsurface geology and provides input into subsequent flow simulations.

  9. 3D Geologic Modeling of the Southern San Joaquin Basin for the Westcarb Kimberlina Demonstration Project- A Status Report

    SciTech Connect

    Wagoner, J

    2009-04-24

    The objective of the Westcarb Kimberlina pilot project is to safely inject 250,000 t CO{sub 2}/yr for four years into the deep subsurface at the Clean Energy Systems (CES) Kimberlina power plant in southern San Joaquin Valley, California. In support of this effort, we have constructed a regional 3D geologic model of the southern San Joaquin basin. The model is centered on the Kimberlina power plant and spans the UTM range E 260000-343829 m and N 3887700-4000309 m; the depth of the model ranges from the topographic surface to >9000 m below sea level. The mapped geologic units are Quaternary basin fill, Tertiary marine and continental deposits, and pre-Tertiary basement rocks. Detailed geologic data, including surface maps, borehole data, and geophysical surveys, were used to define the geologic framework. Fifteen time-stratigraphic formations were mapped, as well as >140 faults. The free surface is based on a 10 m lateral resolution DEM. We use Earthvision (Dynamic Graphics, Inc.) to integrate the geologic and geophysical information into a 3D model of x,y,z,p nodes, where p is a unique integer index value representing the geologic unit. This grid represents a realistic model of the subsurface geology and provides input into subsequent flow simulations.

  10. 3D mapping of geological contacts by coupling Aerial Laser Scanning, Gigapixel photography and open access pictures

    NASA Astrophysics Data System (ADS)

    Nguyen, Liliane; Guerin, Antoine; Abellán, Antonio; Carrea, Dario; Derron, Marc-Henri; Jaboyedoff, Michel

    2015-04-01

    Multiple sources of geological data exist nowadays, most of them are in 2D (e.g. geological maps, geological panoramic sketch), and only a few are in 3D (e.g. block diagram). One of the current challenges in geological mapping consists not only in providing a more consistent 3D data, but also in pursuing a gathering and a harmonisation of the geological information in order to obtain a more consistent interpretations of the 3D geological models. New remote sensing techniques have significantly improved the representation of three-dimensional surfaces during the last decade, especially for steep and inaccessible rockcliffs. Therefore, we present an exploratory study aiming to find a reliable method for carrying out a three-dimensional mapping of geological contacts using a High Resolution Digital Elevation Model (HRDEM) with a 1 meter cell size. To this end, we selected the "Scex Rouge Mountain" as pilot study area. This outcrop, which is located in the Diablerets Massif (Vaud, Swiss Alps), has the particularity to present very distinguishable folded geological boundaries on its Southern face. The Southern slope belongs to the Wildhorn nappe, which is mainly composed of sedimentary rocks. The top-layer is composed of siliceous limestones, the well-visible fold layer is the "Pygurus layer" and consist of sandy limestone. Finally the bottom-layer includes marly schist and clayey limestones. At first, different sources of information has been draped on the HRDEM of the Scex Rouge Mountain, including not only classical geological maps (1:25 000) but also different sources of imagery (e.g. gigapixel panoramas, open access images, etc.). In a second step, several three-dimensional polylines have been drawn following the geological limit on each drapped HRDEM. Then we investigated the accuracy of 2D classical geological maps by comparing these geological limits with the drawn 3D polylines. Furthermore, in order to evaluate the accuracy of the method, a ground truth needs

  11. Digital structural interpretation of mountain-scale photogrammetric 3D models (Kamnik Alps, Slovenia)

    NASA Astrophysics Data System (ADS)

    Dolžan, Erazem; Vrabec, Marko

    2015-04-01

    From the earliest days of geological science, mountainous terrains with their extreme topographic relief and sparse to non-existent vegetation were utilized to a great advantage for gaining 3D insight into geological structure. But whereas Alpine vistas may offer perfect panoramic views of geology, the steep mountain slopes and vertical cliffs make it very time-consuming and difficult (if not impossible) to acquire quantitative mapping data such as precisely georeferenced traces of geological boundaries and attitudes of structural planes. We faced this problem in mapping the central Kamnik Alps of northern Slovenia, which are built up from Mid to Late Triassic succession of carbonate rocks. Polyphase brittle tectonic evolution, monotonous lithology and the presence of temporally and spatially irregular facies boundary between bedded platform carbonates and massive reef limestones considerably complicate the structural interpretation of otherwise perfectly exposed, but hardly accessible massif. We used Agisoft Photoscan Structure-from-Motion photogrammetric software to process a series of overlapping high-resolution (~0.25 m ground resolution) vertical aerial photographs originally acquired by the Geodetic Authority of the Republic of Slovenia for surveying purposes, to derive very detailed 3D triangular mesh models of terrain and associated photographic textures. Phototextures are crucial for geological interpretation of the models as they provide additional levels of detail and lithological information which is not resolvable from geometrical mesh models alone. We then exported the models to Paradigm Gocad software to refine and optimize the meshing. Structural interpretation of the models, including mapping of traces and surfaces of faults and stratigraphic boundaries and determining dips of structural planes, was performed in MVE Move suite which offers a range of useful tools for digital mapping and interpretation. Photogrammetric model was complemented by

  12. 3D thermo-mechanical model of the orogeny in Pamir constrained by geological and geophysical observations

    NASA Astrophysics Data System (ADS)

    Sobolev, S. V.; Tympel, J.; Ratschbacher, L.

    2015-12-01

    The Pamir-Hindu Kush orogenic belt is the result of the indentation of the western corner of the India plate into Eurasia. It has accommodated the highest strain over the shortest meridional distance of the India-Eurasia collision zone. Recent high-resolution seismic tomographic and receiver function studies confirm the presence of a south-dipping continental lithosphere, which has been traced to the depth of more than 200-300 km beneath the northern Pamir (Pamir slab). Balanced cross-section document crustal shortening associated with the corresponding frontal thrust system of a few tens of km, which is much less than the expected (>200-300 km) for intra-continental subduction zone, based on the seismically imaged length of the Pamir slab. Another unique feature of Pamir is the presence of large gneiss domes with the exhumation reaching a depth of 30-40 km.We employ the finite-element thermomechanical modelling technique SLIM3D to simulate the evolution of the Pamir orogeny during the last 25 Myr. The technique is using advanced non-linear elasto-visco-plastic rheology with parameters based on laboratory experiments. Our 3D model extends 1100 km N-S, 800 km E-W, and 300 km deep, and replicates indentation of the western half of India promontory into Eurasia. The moving modelling-window technique allows focusing at the most extensively deforming domains, and a 3D model setup and boundary conditions allow lateral material flow to the west, i.e. perpendicular to the direction of tectonic shortening.The model replicates major features of the lithospheric structure and geological history. For instance, we demonstrate that large part of the roll back of the Pamir slab may be caused by the delamination of the mantle lithosphere together with the lower crust, rather than classical intra-continental subduction involving thrust-imbrication of the uppermost crust. The resulting shortening at the Pamir frontal thrust system appears to be lower than 50 km in accord with

  13. 3D Geological Modeling of CoalBed Methane (CBM) Resources in the Taldykuduk Block Karaganda Coal Basin, Kazakhstan

    NASA Astrophysics Data System (ADS)

    Sadykov, Raman; Kiponievich Ogay, Evgeniy; Royer, Jean-Jacques; Zhapbasbayev, Uzak; Panfilova, Irina

    2015-04-01

    Coal Bed Methane (CBM) is gas stored in coal layers. It can be extracted from wells after hydraulic fracturing and/or solvent injection, and secondary recovery techniques such as CO2 injection. Karaganda Basin is a very favorable candidate region to develop CBM production for the following reasons: (i) Huge gas potential; (ii) Available technologies for extracting and commercializing the gas produced by CBM methods; (iii) Experience in degassing during underground mining operations for safety reasons; (iv) Local needs in energy for producing electricity for the industrial and domestic market. The objectives of this work are to model the Taldykuduk block coal layers and their properties focusing on Coal Bed Methane production. It is motivated by the availability of large coal bed methane resources in Karaganda coal basin which includes 4 300 Bm3 equivalent 2 billion tons of coal (B = billion = 109) with gas content 15-25 m3/t of coal (for comparison San Juan basin (USA) has < 20 m3/t). The CBM reserves estimations are about: Saransk block, 26.3 Bm3 and Taldykuduk block, 23.5 Bm3. Methane (CH4) can be considered as an environmentally-friendly fuel compared to coal. Actually, the methane extracted during mining is released in the atmosphere, collecting it for recovering energy will reduce CO2 equivalent emissions by 36 Mt, good news regarding climate warming issues. The exploitation method will be based on a EOR technology consisting in injecting CO2 which replaces methane in pores because it has a higher adsorption capacity than CH4; exploiting CBM by CO2 injection provides thus a safe way to sequestrate CO2 in adsorbed form. The 3D geological model was built on Gocad/Skua using the following available data set: 926 wells and large area (7 x 12 km). No seismic data; coal type and chemical components (S, ash, …); unreliable available cross-section & maps due to old acquisition; quality mature coal; complex heterogeneous fractures network reported on geological cross

  14. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

    Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.; Smith, Collin S.

    2015-09-01

    Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capability are discussed.

  15. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

    Structured light 3D surface imaging has been crucial in the fields of image processing and computer vision, particularly in reconstruction, recognition and others. In this dissertation, we propose the approaches to development of an efficient 3D surface imaging system using structured light patterns including reconstruction, recognition and sampling criterion. To achieve an efficient reconstruction system, we address the problem in its many dimensions. In the first, we extract geometric 3D coordinates of an object which is illuminated by a set of concentric circular patterns and reflected to a 2D image plane. The relationship between the original and the deformed shape of the light patterns due to a surface shape provides sufficient 3D coordinates information. In the second, we consider system efficiency. The efficiency, which can be quantified by the size of data, is improved by reducing the number of circular patterns to be projected onto an object of interest. Akin to the Shannon-Nyquist Sampling Theorem, we derive the minimum number of circular patterns which sufficiently represents the target object with no considerable information loss. Specific geometric information (e.g. the highest curvature) of an object is key to deriving the minimum sampling density. In the third, the object, represented using the minimum number of patterns, has incomplete color information (i.e. color information is given a priori along with the curves). An interpolation is carried out to complete the photometric reconstruction. The results can be approximately reconstructed because the minimum number of the patterns may not exactly reconstruct the original object. But the result does not show considerable information loss, and the performance of an approximate reconstruction is evaluated by performing recognition or classification. In an object recognition, we use facial curves which are deformed circular curves (patterns) on a target object. We simply carry out comparison between the

  16. Improved hybrid optimization algorithm for 3D protein structure prediction.

    PubMed

    Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

    2014-07-01

    A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins. PMID:25069136

  17. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

    Coronal Mass Ejections (CMEs) represent one of the most powerful energy release phenomena in the entire solar system and are a major driver of space weather. Prior to 2006, our observational access to CMEs was limited to single viewpoint remote sensing observations in the inner/outer corona, and in-situ observations further away, e.g. at 1 AU. Taking all these factors together, turned out to be a major obstacle in our understanding and characterizing of the 3D structure and evolution of CMEs. The situation improved dramatically with the availability of multi-viewpoint imaging observations of CMEs, all way through from the Sun to 1 AU, from the STEREO mission since 2006, combined with observations from other missions (SOHO, Hinode, SDO, IRIS). With this talk we will discuss several key recent results in CME science resulting from the analysis of multi-viewpoint observations. This includes: (1) shape and structure; (2) kinematics and energetics; (3) trajectories, deflections and rotations; (4) arrival times and velocities at 1 AU; (5) magnetic field structure; (6) relationships with coronal and interplanetary shocks and solar energetic particles. The implications of these results in terms of CME theories and models will be also addressed. We will conclude with a discussion of important open issues in our understanding of CMEs and how these could be addressed with upcoming (Solar Orbiter, Solar Probe Plus) and under-study missions (e.g., L5).

  18. 3D Geo-Structures Visualization Education Project (3dgeostructuresvis.ucdavis.edu)

    NASA Astrophysics Data System (ADS)

    Billen, M. I.

    2014-12-01

    Students of field-based geology must master a suite of challenging skills from recognizing rocks, to measuring orientations of features in the field, to finding oneself (and the outcrop) on a map and placing structural information on maps. Students must then synthesize this information to derive meaning from the observations and ultimately to determine the three-dimensional (3D) shape of the deformed structures and their kinematic history. Synthesizing this kind of information requires sophisticated visualizations skills in order to extrapolate observations into the subsurface or missing (eroded) material. The good news is that students can learn 3D visualization skills through practice, and virtual tools can help provide some of that practice. Here I present a suite of learning modules focused at developing students' ability to imagine (visualize) complex 3D structures and their exposure through digital topographic surfaces. Using the software 3DVisualizer, developed by KeckCAVES (keckcaves.org) we have developed visualizations of common geologic structures (e.g., syncline, dipping fold) in which the rock is represented by originally flat-lying layers of sediment, each with a different color, which have been subsequently deformed. The exercises build up in complexity, first focusing on understanding the structure in 3D (penetrative understanding), and then moving to the exposure of the structure at a topographic surface. Individual layers can be rendered as a transparent feature to explore how the layer extends above and below the topographic surface (e.g., to follow an eroded fold limb across a valley). The exercises are provided using either movies of the visualization (which can also be used for examples during lectures), or the data and software can be downloaded to allow for more self-driven exploration and learning. These virtual field models and exercises can be used as "practice runs" before going into the field, as make-up assignments, as a field

  19. CARd-3D: Carbon Distribution in 3D Structure Program for Globular Proteins

    PubMed Central

    Ekambaram, Rajasekaran; Kannaiyan, Akila; Marimuthu, Vijayasarathy; Swaminathan, Vinobha Chinnaiah; Renganathan, Senthil; Perumal, Ananda Gopu

    2014-01-01

    Spatial arrangement of carbon in protein structure is analyzed here. Particularly, the carbon fractions around individual atoms are compared. It is hoped that it follows the principle of 31.45% carbon around individual atoms. The results reveal that globular protein's atoms follow this principle. A comparative study on monomer versus dimer reveal that carbon is better distributed in dimeric form than in its monomeric form. Similar study on solid versus liquid structures reveals that the liquid (NMR) structure has better carbon distribution over the corresponding solid (X-Ray) structure. The carbon fraction distributions in fiber and toxin protein are compared. Fiber proteins follow the principle of carbon fraction distribution. At the same time it has another broad spectrum of carbon distribution than in globular proteins. The toxin protein follows an abnormal carbon fraction distribution. The carbon fraction distribution plays an important role in deciding the structure and shape of proteins. It is hoped to help in understanding the protein folding and function. PMID:24748753

  20. 3D geological modeling of the Kasserine Aquifer System, Central Tunisia: New insights into aquifer-geometry and interconnections for a better assessment of groundwater resources

    NASA Astrophysics Data System (ADS)

    Hassen, Imen; Gibson, Helen; Hamzaoui-Azaza, Fadoua; Negro, François; Rachid, Khanfir; Bouhlila, Rachida

    2016-08-01

    The challenge of this study was to create a 3D geological and structural model of the Kasserine Aquifer System (KAS) in central Tunisia and its natural extension into north-east Algeria. This was achieved using an implicit 3D method, which honors prior geological data for both formation boundaries and faults. A current model is presented which provides defendable predictions for the spatial distribution of geology and water resources in aquifers throughout the model-domain. This work has allowed validation of regional scale geology and fault networks in the KAS, and has facilitated the first-ever estimations of groundwater resources in this region by a 3D method. The model enables a preliminary assessment of the hydraulic significance of the major faults by evaluating their influence and role on groundwater flow within and between four compartments of the multi-layered, KAS hydrogeological system. Thus a representative hydrogeological model of the study area is constructed. The possible dual nature of faults in the KAS is discussed in the context that some faults appear to be acting both as barriers to horizontal groundwater flow, and simultaneously as conduits for vertical flow. Also discussed is the possibility that two flow directions occur within the KAS, at a small syncline area of near Feriana. In summary, this work evaluates the influence of aquifer connectivity and the role of faults and geology in groundwater flow within the KAS aquifer system. The current KAS geological model can now be used to guide groundwater managers on the best placement for drilling to test and further refine the understanding of the groundwater system, including the faults connectivity. As more geological data become available, the current model can be easily edited and re-computed to provide an updated model ready for the next stage of investigation by numerical flow modeling.

  1. Earthquake relocation using a 3D a-priori geological velocity model from the western Alps to Corsica: Implication for seismic hazard

    NASA Astrophysics Data System (ADS)

    Béthoux, Nicole; Theunissen, Thomas; Beslier, Marie-Odile; Font, Yvonne; Thouvenot, François; Dessa, Jean-Xavier; Simon, Soazig; Courrioux, Gabriel; Guillen, Antonio

    2016-02-01

    The region between the inner zones of the Alps and Corsica juxtaposes an overthickened crust to an oceanic domain, which makes difficult to ascertain the focal depth of seismic events using routine location codes and average 1D velocity models. The aim of this article is to show that, even with a rather lose monitoring network, accurate routine locations can be achieved by using realistic 3D modelling and advanced location techniques. Previous earthquake tomography studies cover the whole region with spatial resolutions of several tens of kilometres on land, but they fail to resolve the marine domain due to the absence of station coverage and sparse seismicity. To overcome these limitations, we first construct a 3D a-priori P and S velocity model integrating known geophysical and geological information. Significant progress has been achieved in the 3D numerical modelling of complex geological structures by the development of dedicated softwares (e.g. 3D GeoModeller), capable at once of elaborating a 3D structural model from geological and geophysical constraints and, possibly, of refining it by inversion processes (Calcagno et al., 2008). Then, we build an arrival-time catalogue of 1500 events recorded from 2000 to 2011. Hypocentres are then located in this model using a numerical code based on the maximum intersection method (Font et al., 2004), updated by Theunissen et al. (2012), as well as another 3D location technique, the NonLinLoc software (Lomax and Curtis, 2001). The reduction of arrival-time residuals and uncertainties (dh, dz) with respect to classical 1D locations demonstrates the improved accuracy allowed by our approach and confirms the coherence of the 3D geological model built and used in this study. Our results are also compared with previous works that benefitted from the installation of dense temporary networks surrounding the studied epicentre area. The resulting 3D location catalogue allows us to improve the regional seismic hazard assessment

  2. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

    Hopf, Thomas A.; Colwell, Lucy J.; Sheridan, Robert; Rost, Burkhard; Sander, Chris; Marks, Debora S.

    2012-01-01

    Summary We show that amino acid co-variation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this technique to predict previously unknown, 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. The prediction method (EVfold_membrane), applies a maximum entropy approach to infer evolutionary co-variation in pairs of sequence positions within a protein family and then generates all-atom models with the derived pairwise distance constraints. We benchmark the approach with blinded, de novo computation of known transmembrane protein structures from 23 families, demonstrating unprecedented accuracy of the method for large transmembrane proteins. We show how the method can predict oligomerization, functional sites, and conformational changes in transmembrane proteins. With the rapid rise in large-scale sequencing, more accurate and more comprehensive information on evolutionary constraints can be decoded from genetic variation, greatly expanding the repertoire of transmembrane proteins amenable to modelling by this method. PMID:22579045

  3. From new generation of remote sensing geological maps to 3-D model: the Central Kyzylkum (Western Uzbekistan) is taken as example

    NASA Astrophysics Data System (ADS)

    Sidorova, Elena

    2013-04-01

    the recognition of linear and ring features. The features of geological interest detected during the interpretation process were digitized using raster based GIS software. As results of collaboration between GIS and RS data analysis the new prospect areas were extracted from the study areas. Were revealed the geological structures in 3-D model, associated with mineralization, lineaments and ring structures. The complex analysis of model allowed proposing new potential ore areas for statement of prospecting work.

  4. 3-D Structure of the Slave and Rae Cratons Provides Clues to Their Construction

    NASA Astrophysics Data System (ADS)

    Snyder, D. B.

    2013-12-01

    Deep geologic structures within cratons that make up continental cores were long neglected. Recently acquired geophysical data from large observational arrays and geochemical data resulting from exploration for diamond has now made possible co-registration of large-scale (400-km depth), truly 3-dimensional data sets. P-waves, surface waves and magnetotelluric observations provide 3-D wavespeed and conductivity models. Multi-azimuthal receiver functions map seismic discontinuity surfaces in 3-D. Xenolith suites erupted in kimberlites provide rock samples at key lithospheric depths, albeit at sparsely distributed locations. These multi-disciplinary models are becoming available for several key cratons worldwide; here the deep structure of the Slave and Rae cratons of the Canadian Shield is described. Lithospheric layers with tapered, wedge-shaped margins are common. Slave craton layers are sub-horizontal and indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. The central Rae craton has predominantly dipping discontinuities that indicate construction at 1.9 Ga by thrusting similar to that observed in crustal ';thick-skinned' fold-and-thrust belts. 3-D mapping of conductivity and metasomatism, the latter via mineral recrystallization and resetting of isotopic ages, overprints primary structures in both cratons. Distribution of more conductivitve mantle suggests that assumed causative pervasive metasomatism occurs at 100-200 km depths with ';chimneys' reaching to shallower depths, typically in locations where kimberlites or mineralization has occurred.

  5. 3D geological modeling of the transboundary basin Berzdof-Radomierzyce in Upper Lusatia (Germany/Poland)

    NASA Astrophysics Data System (ADS)

    Woloszyn, Iwona; Merkel, Broder; Stanek, Klaus

    2015-04-01

    Keywords: Numerical modeling, Paradigm GOCAD, Berzdorf basin (Germany), Radomierzyce basin (Poland), Upper Lusatia. The accuracy of three-dimensional (3D) models depends on their data density and quality. Regions with a complex geology can be a challenge to model, especially if detailed models are required to support a further economic exploitation of a region. In this research, a 3D model was created based on the region's complicated geological condition. The focus area, the Berzdorf - Radomierzyce basin, located in Upper Lusatia on the Polish - German border to the south of the city of Görlitz - Zgorzelec, is such a region. The basin is divided by the volcanic threshold into the western part (Berzdorf basin) and its eastern extension (Radomierzyce basin). The connection between both parts is the so called "lignite bridge". The deposit in the Berzdorf has been exploited from 1830 until 1997. In contrast, the Radomierzyce deposit has never been exploited and is still considered as a prospective deposit for the operating Turów coal mine, which is located only around 15 km from the deposit. To represent the geology of the area a 3D modeling of the transboundary deposit was carried out. Moreover, some strategies to overcome numerical interpolation instability of the geological model with many faults were developed. Due to the large amount of data and its compatibility with other software the 3D geomodeling software Paradigm GOCAD was used. A total number of 10,102 boreholes, 60 cross sections and geological maps converted into digital format - were implemented into the model. The data density of the German part of the area of interest was much higher than the data density of the Polish part. The results demonstrate a good fit between the modeled surfaces and the real geological conditions. This is particularly evident by matching the modeled surfaces to borehole data and geological cross sections. Furthermore, simplification of the model does not decrease the

  6. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

    Tarquis, A. M.; Gonzalez-Nieto, P. L.; Bird, N. R. A.

    2012-04-01

    Soil voids manifest the cumulative effect of local pedogenic processes and ultimately influence soil behavior - especially as it pertains to aeration and hydrophysical properties. Because of the relatively weak attenuation of X-rays by air, compared with liquids or solids, non-disruptive CT scanning has become a very attractive tool for generating three-dimensional imagery of soil voids. One of the main steps involved in this analysis is the thresholding required to transform the original (greyscale) images into the type of binary representation (e.g., pores in white, solids in black) needed for fractal analysis or simulation with Lattice-Boltzmann models (Baveye et al., 2010). The objective of the current work is to apply an innovative approach to quantifying soil voids and pore networks in original X-ray CT imagery using Relative Entropy (Bird et al., 2006; Tarquis et al., 2008). These will be illustrated using typical imagery representing contrasting soil structures. Particular attention will be given to the need to consider the full 3D context of the CT imagery, as well as scaling issues, in the application and interpretation of this index.

  7. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

    Previous studies have indicated that 2D, time accurate computations based on a pseudo-laminar zonal model of the slat cove region (within the framework of the Reynolds-Averaged Navier-Stokes equations) are inadequate for predicting the full unsteady dynamics of the slat cove flow field. Even though such computations could capture the large-scale, unsteady vorticity structures in the slat cove region without requiring any external forcing, the simulated vortices were excessively strong and the recirculation zone was unduly energetic in comparison with the PIV measurements for a generic high-lift configuration. To resolve this discrepancy and to help enable physics based predictions of slat aeroacoustics, the present paper is focused on 3D simulations of the slat cove flow over a computational domain of limited spanwise extent. Maintaining the pseudo-laminar approach, current results indicate that accounting for the three-dimensionality of flow fluctuations leads to considerable improvement in the accuracy of the unsteady, nearfield solution. Analysis of simulation data points to the likely significance of turbulent fluctuations near the reattachment region toward the generation of broadband slat noise. The computed acoustic characteristics (in terms of the frequency spectrum and spatial distribution) within short distances from the slat resemble the previously reported, subscale measurements of slat noise.

  8. An implicit dispersive transport algorithm for the US Geological Survey MOC3D solute-transport model

    USGS Publications Warehouse

    Kipp, K.L., Jr.; Konikow, L.F.; Hornberger, G.Z.

    1998-01-01

    This report documents an extension to the U.S. Geological Survey MOC3D transport model that incorporates an implicit-in-time difference approximation for the dispersive transport equation, including source/sink terms. The original MOC3D transport model (Version 1) uses the method of characteristics to solve the transport equation on the basis of the velocity field. The original MOC3D solution algorithm incorporates particle tracking to represent advective processes and an explicit finite-difference formulation to calculate dispersive fluxes. The new implicit procedure eliminates several stability criteria required for the previous explicit formulation. This allows much larger transport time increments to be used in dispersion-dominated problems. The decoupling of advective and dispersive transport in MOC3D, however, is unchanged. With the implicit extension, the MOC3D model is upgraded to Version 2. A description of the numerical method of the implicit dispersion calculation, the data-input requirements and output options, and the results of simulator testing and evaluation are presented. Version 2 of MOC3D was evaluated for the same set of problems used for verification of Version 1. These test results indicate that the implicit calculation of Version 2 matches the accuracy of Version 1, yet is more efficient than the explicit calculation for transport problems that are characterized by a grid Peclet number less than about 1.0.

  9. Developing a geological 3D model for the Tanour and Rasoun spring catchment area using ArcGIS and GOCAD

    NASA Astrophysics Data System (ADS)

    Hamdan, Ibraheem; Benhsinat, Mohamed; Wagner, Bianca; Sauter, Martin

    2016-04-01

    Key words: Karst, 3D model, GOCAD, ArcGIS, Jordan. Tanour and Rasoun karst springs (around 75 km northwest of the capital city of Amman in Jordan) are used as main local water supply for the surrounding villages. Carbonate rocks are the predominant rock type in the study area (Upper Cretaceous age). The karstification degree is moderate to high, with the availability of different karst features like dolines, caves, dry valleys, and highly fractured rocks. During the last years, the water supply from these springs had to be disconnected for several times due to microbial contamination and waste water pollution from local olive oil mills. For better understanding of the geological and the hydrogeological setting of the study area, in addition to the delineation of the groundwater catchment area for Tanour and Rasoun springs, a geological 3D model of the main geological formations within the study area was established using ArcGIS and GOCAD. The model is based on geological maps and well data; it was established for seven geological layers that act as prominent aquifers and aquicludes. ArcGIS software was used for data preparation, processing and interpolation of varying thickness, while GOCAD used for geometrical modeling steps. After the completion of the first modeling steps, major faults are included. Then the subsurface catchments will be delineated and compared with the superficial watersheds. The model still under development and open for further development.

  10. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

    Freymark, Jessica; Sippel, Judith; Scheck-Wenderoth, Magdalena; Bär, Kristian; Stiller, Manfred; Fritsche, Johann-Gerhard; Kracht, Matthias

    2016-04-01

    The Upper Rhine Graben (URG) was formed as part of the European Cenozoic Rift System in a complex extensional setting. At present-day, it has a large socioeconomic relevance as it provides a great potential for geothermal energy production in Germany and France. For the utilisation of this energy resource it is crucial to understand the structure and the observed temperature anomalies in the rift basin. In the framework of the EU-funded "IMAGE" project (Integrated Methods for Advanced Geothermal Exploration), we apply a data-driven numerical modelling approach to quantify the processes and properties controlling the spatial distribution of subsurface temperatures. Typically, reservoir-scale numerical models are developed for predictions on the subsurface hydrothermal conditions and for reducing the risk of drilling non-productive geothermal wells. One major problem related to such models is setting appropriate boundary conditions that define, for instance, how much heat enters the reservoir from greater depths. Therefore, we first build a regional lithospheric-scale 3D structural model, which covers not only the entire URG but also adjacent geological features like the Black Forest and the Vosges Mountains. In particular, we use a multidisciplinary dataset (e.g. well data, seismic reflection data, existing structural models, gravity) to construct the geometries of the sediments, the crust and the lithospheric mantle that control the spatial distribution of thermal conductivity and radiogenic heat production and hence temperatures. By applying a data-based and lithology-dependent parameterisation of this lithospheric-scale 3D structural model and a 3D finite element method, we calculate the steady-state conductive thermal field for the entire region. Available measured temperatures (down to depths of up to 5 km) are considered to validate the 3D thermal model. We present major characteristics of the lithospheric-scale 3D structural model and results of the 3D

  11. Building a 3D geological near surface model from borehole and laboratory data

    NASA Astrophysics Data System (ADS)

    Sala, P.; Tisato, N.; Pfiffner, O. A.; Frehner, M.

    2012-04-01

    The interpretation of active seismic survey data usually results in a subsurface P-wave velocity model. Such models commonly do not include the near surface, but end a few hundreds of meters beneath the Earth's surface. However, near surface effects, such as low-velocity zones or topography can influence the seismic signal significantly. Therefore, it is important to extend the P-wave velocity model all the way to the Earth's surface. As a test site of this study, we use the underground gas storage facility in Chémery (France), located at the south-western border of the Paris Basin. Velocities and lithological data of the shallow formations can be found in a public dataset, which collects data of a large number of short boreholes (BRGM online catalog: infoterre.brgm.fr/viewer). From the lithological data a structural model defined by surfaces gridded from well markers and faults derived from the analysis of these surfaces, is generated. The generation of the structural model comprised some major challenges, mainly because the borehole data represent 1D vertical pinpoints into the subsurface, rather than 2D sections as it is the case for most seismic surveys. This complicated the cross-correlation between the boreholes and the interpolation of the lithological formations in the 3D space. After the structural model has been generated, the velocity logs were upscaled to the model and interpolated to generate a near-surface P wave velocity model. To better constrain the velocity model, laboratory measurements of P-wave velocity were conducted. We collected 24 hand specimens from outcrops, from which we drilled core plugs. The sampled lithologies are 6 different sedimentary rock types, mostly calcarenites. The measurements were conducted employing the pulse transmission method for compression (Vp) and shear (Vs) waves in dry and fully water saturated conditions. Density and porosity were measured with two different methods: (1) with a helium pycnometer, and (2

  12. Characterization of the Hontomín Research Facility for Geological Storage of CO2: 3D Seismic Imaging Results

    NASA Astrophysics Data System (ADS)

    Alcalde, J.; Martí, D.; Juhlin, C.; Malehmir, A.; Calahorrano, A.; Ayarza, P.; Pérez-Estaún, A.; Carbonell, R.

    2012-04-01

    A technological research facility dedicated to the underground geological storage of CO2 is currently being developed by the Spanish research program on Carbon Capture and Storage (CCS) in Hontomin (Burgos). This research program is being developed by the CIUDEN Foundation, an initiative launched by 3 Spanish state departments (Science & Innovation, Environment and Industry). An extensive multidisciplinary site characterization phase has been carried out, including a multiseismic data acquisition experiment. Within this effort, a 36 km2 3D seismic reflection survey was acquired in the summer of 2010. Its aim was to provide high resolution images of the subsurface of the storage complex, as well as to provide a baseline model for all the disciplines involved in the project. The target reservoir is a saline aquifer located at 1400 m, approximately, within Lower Jurassic carbonates (Lias). The main seal is formed by inter-layered marls and marly limestones of Early to Middle Jurassic age (Dogger and Lias). The main acquisition characteristics of the survey included (1) a mixed source of vibroseis and explosives with 74% and 26% of each used, respectively, (2) 5000 source points distributed along 22 source lines (separated 250 m) and (3) 22 lines of receivers (separated 275 m). Shot and receiver spacing along the source and receiver lines was 25 m, resulting in a nominal CDP-fold of 36 for 13 m2 bins. The 3D-data have been fully processed to post stack migration. The most critical processing steps included static correction calculations, time variant frequency filtering, rms velocity analysis, F-XY deconvolution, dip move-out correction, residual statics calculations and post stack migration. The final high-resolution 3D-volume shows the shape and depth of the primary reservoir-seal system, the main faults of the area and the secondary reservoir-seal sequence. It allows us to characterize the main tectonic structure of the dome complex, the fault system of the area and

  13. The southeastern border of the Upper Rhine Graben: a 3D geological model and its importance for tectonics and groundwater flow

    NASA Astrophysics Data System (ADS)

    Spottke, Ina; Zechner, Eric; Huggenberger, Peter

    2005-09-01

    A 3D geological model of the area east of Basel on the southeastern border of the Upper Rhine Graben, consisting of 47 faults and six stratigraphic horizons relevant for groundwater flow, was developed using borehole data, geological maps, geological cross sections, and outcrop data. This model provides new insight into the discussions about the kinematics of the area between the southeastern border of the Upper Rhine Graben and the Tabular Jura east of Basel. A 3D analysis showed that both thin-skinned and thick-skinned tectonic elements occur in the modeled area and that the Anticline and a series of narrow graben structures developed simultaneously during an extensional stress-field varying from E W to SSE NNW, which lasted from the Middle Eocene to Late Oligocene. In a new approach the faults and horizons of the 3D geological model were transferred into discrete elements with distributed hydrogeological properties in order to simulate the 3D groundwater flow regime within the modeled aquifers. A three-layer approach with a horizontal regularly spaced grid combined with an irregular property distribution of transmissivity in depth permitted the piezometric head of the steady-state model to be automatically calibrated to corresponding measurements using more than 200 piezometers. Groundwater modeling results demonstrated that large-scale industrial pumping affected the groundwater flow field in the Upper Muschelkalk aquifer at distances of up to 2 km to the south. The results of this research will act as the basis for further model developments, including salt dissolution and solute transport in the area, and may ultimately help to provide predictions for widespread land subsidence risks.

  14. 3-D Multiphase Segmentation of X-Ray Micro Computed Tomography Data of Geologic Materials

    NASA Astrophysics Data System (ADS)

    Tuller, M.; Kulkarni, R.; Fink, W.

    2011-12-01

    Advancements of noninvasive imaging methods such as X-Ray Computed Tomography (CT) led to a recent surge of applications in Geoscience. While substantial efforts and resources have been devoted to advance CT technology and micro-scale analysis, the development of a stable 3-D multiphase image segmentation method applicable to large datasets is lacking. To eliminate the need for wet/dry or dual energy scans, image alignment, and subtraction analysis, commonly applied in synchrotron X-Ray micro CT, a segmentation method based on a Bayesian Markov Random Field (MRF) framework amenable to true 3-D multiphase processing was developed and evaluated. Furthermore, several heuristic and deterministic combinatorial optimization schemes required to solve the labeling problem of the MRF image model were implemented and tested for computational efficiency and their impact on segmentation results. Test results for natural and artificial porous media datasets demonstrate great potential of the MRF image model for 3-D multiphase segmentation.

  15. Cognitive 3D geological voxel modelling based on AEM and seismic data - a case from the southern part of Denmark

    NASA Astrophysics Data System (ADS)

    Jørgensen, Flemming; Møller, Rasmus R.; Sandersen, Peter B. E.; Høyer, Anne-Sophie

    2013-04-01

    The highly complex composition of the Quaternary and Tertiary near-surface deposits in Denmark is a challenging environment for 3D modelling. Geological elements like cross-cutting buried valleys, faults, glaciotectonic thrusts and folds, delta units and erosional unconformities are vital to identify and include in 3D geological models, but at the same time they all add to the complexity of the geological picture. Borehole data are rarely sufficient for the modelling; instead much more laterally dense data are needed. Airborne electromagnetic techniques therefore serve as perfect tools for providing an overview and spatial distribution of the geological elements and their composition. Such airborne surveys are perfectly supplemented by seismic data in order to map the stratigraphic framework within a model area. Translating airborne electromagnetic data to geology is a complicated task that requires a significant amount of geophysical and geological insight. It is necessary to implement thorough geological background knowledge in the interpretations while at the same time identify and acknowledge the inherent limitations of the method. In an area covering 730 km2 across the border between Germany and Denmark a combination of an airborne transient electromagnetic survey (3200 line km performed with the SkyTEM system) and a 38 km high-resolution 2D seismic survey has proven very successful for mapping geological elements like the above-mentioned. Although the south-westernmost part of the study area is saturated with saltwater and the TEM data therefore are influenced by increased electrical conductivity, the geology is still revealed here. Geological interpretations are supported by a high number of pre-existing seismic sections originating from hydrocarbon exploration and borehole data, though most of the borehole data and several of the seismic sections have very poor quality. A couple of new 300-m deep exploration boreholes have been drilled in order to obtain

  16. Mapping the North Sea base-Quaternary: using 3D seismic to fill a gap in the geological record

    NASA Astrophysics Data System (ADS)

    Lamb, Rachel; Huuse, Mads; Stewart, Margaret; Brocklehurst, Simon H.

    2014-05-01

    The identification and mapping of the base-Quaternary boundary in the central parts of the North Sea is problematic due to the change from an unconformable transition between Pliocene and Pleistocene deltaic deposits in the southern North Sea to a conformable one further north (Sejrup et al 1991; Gatliff et al 1994). The best estimates of the transition use seismic reflection data to identify a 'crenulated reflector' (Buckley 2012), or rely on correlating sparse biostratigraphy (Cameron et al 1987). Recent integration of biostratigraphy, pollen analysis, paleomagnetism and amino acid analysis in the Dutch and Danish sectors (Rasmussen et al 2005; Kuhlmann et al 2006) allows greater confidence in the correlation to a regional 3D seismic dataset and show that the base-Quaternary can be mapped across the entire basin. The base-Quaternary has been mapped using the PGS MegaSurvey dataset from wells in the Danish Sector along the initially unconformable horizon and down the delta front into the more conformable basin giving a high degree of confidence in the horizon pick. The mapped horizon is presented here alongside the difference between this new interpretation and the previously interpreted base-Quaternary (Buckley 2012). The revised base-Quaternary surface reaches a depth of 1248 ms TWT or approximately 1120 m (assuming average velocity of 1800 m/s) showing an elongate basin shape that follows the underlying structure of the Central Graben. The difference between the revised base-Quaternary and the traditional base-Quaternary reaches a maximum of over 600 ms TWT or approximately 540 m in the south-west with over 300 ms TWT or approximately 270 m at the Josephine well (56° 36.11'N, 2° 27.09'E) in the centre of the basin. Mapping this new base-Quaternary allows for the interpretation of the paleo-envionrment during the earliest Quaternary. Seismic attribute analysis indicates a deep water basin with sediment deposition from multiple deltas and redistribution by deep

  17. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

    How graphics postprocessing techniques are currently used to examine the results of 3-D nonlinear analyses, some new techniques which take advantage of recent technology, and how these results relate to both the finite element model and its geometric parent are reviewed.

  18. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

    Zanchi, Andrea; Agliardi, Federico; Crosta, Giovanni B.; Villa, Alberto; Bistacchi, Andrea; Iudica, Gaetano

    2015-04-01

    points based on their normal vector orientations to identify and map bedding and fractures. Combined stereographic analysis of bedding orientations and use of filters allowed the quantification of fold hinge and limb geometries and their 3D reconstruction in GOCAD. Fracture patterns derived from points clouds and field data allowed identifying different geomechanical domains associated to the folded structure. Our results encourage the integrated analysis of high-resolution point clouds and detailed structural and geomechanical field data as inputs to the 3D geometrical reconstruction and modelling of folded rock masses. Validation of virtual outcrop reconstructions through a comparison with field structural measurements suggests that very precise geometrical constraints can be obtained by TLS on geological bodies with complex geometrical features. However, additional constraints on TLS survey layout design are required to optimise the reconstruction and distinction of specific structural elements associated to folding as bedding and fold-related fracture systems.

  19. Geological characterization of Italian reservoirs and numerical 3D modelling of CO2 storage scenarios into saline aquifers

    NASA Astrophysics Data System (ADS)

    Beretta, S.; Moia, F.; Guandalini, R.; Cappelletti, F.

    2012-04-01

    The research activities carried out by the Environment and Sustainable Development Department of RSE S.p.A. aim to evaluate the feasibility of CO2 geological sequestration in Italy, with particular reference to the storage into saline aquifers. The identification and geological characterization of the Italian potential storage sites, together with the study of the temporal and spatial evolution of the CO2 plume within the caprock-reservoir system, are performed using different modelling tools available in the Integrated Analysis Modelling System (SIAM) entirely powered in RSE. The numerical modelling approach is the only one that allows to investigate the behaviour of the injected CO2 regarding the fluid dynamic, geochemical and geomechanical aspects and effects due to its spread, in order to verify the safety of the process. The SIAM tools allow: - Selection of potential Italian storage sites through geological and geophysical data collected in the GIS-CO2 web database; - Characterization of caprock and aquifer parameters, seismic risk and environmental link for the selected site; - Creation of the 3D simulation model for the selected domain, using the modeller METHODRdS powered by RSE and the mesh generator GMSH; - Simulation of the injection and the displacement of CO2: multiphase fluid 3D dynamics is based on the modified version of TOUGH2 model; - Evaluation of geochemical reaction effects; - Evaluation of geomechanic effects, using the coupled 3D CANT-SD finite elements code; - Detailed local analysis through the use of open source auxiliary tools, such as SHEMAT and FEHM. - 3D graphic analysis of the results. These numerical tools have been successfully used for simulating the injection and the spread of CO2 into several real Italian reservoirs and have allowed to achieve accurate results in terms of effective storage capacity and safety analysis. The 3D geological models represent the high geological complexity of the Italian subsoil, where reservoirs are

  20. Arbitrary and Parallel Nanofabrication of 3D Metal Structures with Polymer Brush Resists.

    PubMed

    Chen, Chaojian; Xie, Zhuang; Wei, Xiaoling; Zheng, Zijian

    2015-12-01

    3D polymer brushes are reported for the first time as ideal resists for the alignment-free nanofabrication of complex 3D metal structures with sub-100 nm lateral resolution and sub-10 nm vertical resolution. Since 3D polymer brushes can be serially fabricated in parallel, this method is effective to generate arbitrary 3D metal structures over a large area at a high throughput. PMID:26439441

  1. 3D modeling of soil structure in urban groundwater areas: case studies in Kolpene, Rovaniemi, Finland

    NASA Astrophysics Data System (ADS)

    Kupila, Juho

    2015-04-01

    3D modeling of groundwater areas is an important research method in groundwater surveys. Model of geological soil structure improves the knowledge of linkage between land use planning and groundwater protection. Results can be used as base information when developing the water supply services and anticipating and performing the measures needed in case of environmental accidents. Also, collected information is utilized when creating the groundwater flow model. In Finland, structure studies have been conducted in cooperation (among others) with the municipalities and local water suppliers and with the authorities from the Centre for Economic Development, Transport and the Environment. Geological Survey of Finland carries out project "Structure studies in Kolpene groundwater area" in Rovaniemi, Finnish Lapland. Study site is located in northern Finland, in the vicinity of the city center of Rovaniemi. Extent of the area is about 13 square kilometers and there are lots of urban residential areas and other human activities. The objective of this project is to determine the geological structure of the Kolpene groundwater area so that the results can be used to estimate the validity of the present exclusion area and possible risks to the groundwater caused by the land use. Soil layers of the groundwater area are studied by means of collecting information by heavy drilling, geophysical surveying (ground penetrating radar and gravimeter measurements) and water sampling from the installed observation pipes. Also the general geological and hydrological mappings are carried out. Main results which will be produced are: 1) the model of the bedrock surface, 2) the model of the surface of the ground water and flow directions, 3) the thickness of ground water saturated soil layers and 4) location and main characteristics of the soil layers which are significant to the ground water conditions. The preparing studies have been started at the end of 2013 and the results will be

  2. Real-time structured light intraoral 3D measurement pipeline

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

    Computer aided design and manufacturing (CAD/CAM) is increasingly becoming a standard feature and service provided to patients in dentist offices and denture manufacturing laboratories. Although the quality of the tools and data has slowly improved in the last years, due to various surface measurement challenges, practical, accurate, invivo, real-time 3D high quality data acquisition and processing still needs improving. Advances in GPU computational power have allowed for achieving near real-time 3D intraoral in-vivo scanning of patient's teeth. We explore in this paper, from a real-time perspective, a hardware-software-GPU solution that addresses all the requirements mentioned before. Moreover we exemplify and quantify the hard and soft deadlines required by such a system and illustrate how they are supported in our implementation.

  3. Structure of the Rambler Rhyolite, Baie Verte Peninsula, Newfoundland: Inversions using UBC-GIF Grav3D and Mag3D

    NASA Astrophysics Data System (ADS)

    Spicer, B.; Morris, B.; Ugalde, H.

    2011-09-01

    Hosted within the Pacquet Harbour Group (PHG) on the Baie Verte Peninsula of north-central Newfoundland, the Rambler rhyolite is a 487 Ma unit of felsic tuffs, flows and subvolcanic intrusive rocks. The PHG has been affected by multiple phases of deformation with the youngest D4 deformation event producing broad northeast plunging upright cross folds in the Rambler rhyolite. Fold culminations on the upper bounding surface of the rhyolite host Cu +/- Au volcanogenic massive sulfide deposits (e.g. Rambler and Ming mines). Geophysical inversions of recently acquired high resolution gravity and magnetic data have been implemented to determine the extent of the fold axis (dome) at depth. To direct the outcome of the inversion process towards a more geologically reasonable solution this study outlines a procedure which permits the inclusion of known geological and geophysical constraints into the input (reference) model for inversion using the MAG3D and GRAV3D algorithms provided by the University of British Columbia Geophysical Inversion Facility. Reference model constraints included surficial geological contacts as defined by aeromagnetic data, and subsurface distribution of physical property variations from a series of drill-hole logs. The output (computed) model images the surface of the rhyolite dome as dipping roughly 40° to the northeast as a series of voxels with density values ranging from 2.71 to 2.75 g/cm3. While previously published ore deposit models parallel this structure in the near surface, results from these inversions suggest deeper exploration may be favorable. Magnetic inversion modeling has not provided any insight into dome morphology however it outlines the distribution of gabbroic dykes surrounding the dome.

  4. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

    Laser scanning confocal microscopy was used to study the dynamics of 3D assemblies spontaneously formed in microtubule (MT) solutions. Microtubule solutions prepared by mixing and incubating tubulin in the presence of GTP and Oregon Green conjugated taxol in PM buffer were placed in long, sub-millimeter thin glass cells by the capillary action. Within 24 hours, starting with a uniform distribution, microtubules were found to be gradually separated into a few large ``buckled'' bundles along the long direction, and in the middle plane, of the sample cell. A well-defined wavelength of the buckling sinusoids was around 510 μm. The cross section of these round bundles was approximately 40 μm in diameter and the lengths were several centimeters. Detailed analysis of the 3-D image within the bundles revealed that each bundle seemed to consist of loosely packed MTs. It appeared that MTs were phase separated resulting from attractive interactions between charged MT fibers. The ``buckling'' behavior could be the result of geometrical constraints of the repulsive cell walls and the repulsive interaction between bundles. Detailed 3-D observations of the dynamic evolution of MT assembly could provide insight to the mechanisms of cellular MT organization and phase separation of charged colloidal rods.

  5. 3D geological modelling and geothermal mapping - the first results of the transboundary Polish - Saxon project "TransGeoTherm"

    NASA Astrophysics Data System (ADS)

    Kozdrój, Wiesław; Kłonowski, Maciej; Mydłowski, Adam; Ziółkowska-Kozdrój, Małgorzata; Badura, Janusz; Przybylski, Bogusław; Russ, Dorota; Zawistowski, Karol; Domańska, Urszula; Karamański, Paweł; Krentz, Ottomar; Hofmann, Karina; Riedel, Peter; Reinhardt, Silke; Bretschneider, Mario

    2014-05-01

    TransGeoTherm is a common project of the Polish Geological Institute - National Research Institute Lower Silesian Branch (Lead Partner) and the Saxon State Agency for Environment, Agriculture and Geology, co-financed by the European Union (EU) under the framework of the Operational Programme for Transboundary Co-operation Poland-Saxony 2007-2013. It started in October 2012 and will last until June 2014. The main goal of the project is to introduce and establish the use of low temperature geothermal energy as a low emission energy source in the Saxon-Polish transboundary project area. The numerous geological, hydrogeological and geothermal data have been gathered, analysed, combined and interpreted with respect to 3D numerical modelling and subsequently processed with use of the GOCAD software. The resulting geological model covers the transboundary project area exceeding 1.000 km2 and comprises around 70 units up to the depth of about 200 metres (locally deeper) below the terrain. The division of the above units has been based on their litho-stratigraphy as well as geological, hydrogeological and geothermal settings. The model includes two lignite deposits: Berzdorf deposit in Saxony-mined out and already recultivated and Radomierzyce deposit in Poland - documented but still not excavated. At the end of the modelling procedure the raster data sets of the top, bottom and thickness of every unit will be deduced from the 3D geological model with a gridsize of 25 by 25 metres. Based on the geothermal properties of the rocks and their groundwater content a specific value of geothermal conductivity will be allocated to each layer of every borehole. Thereafter for every section of a borehole, belonging to a certain unit of the 3D geological model, a weighted mean value will be calculated. Next the horizontal distribution of these values within every unit will be interpolated. This step / procedure has to be done for all units. As a result of further calculations a series

  6. 3D structure of the Gusev Crater region

    NASA Astrophysics Data System (ADS)

    Parker, Mirjam van Kan; Zegers, Tanja; Kneissl, Thomas; Ivanov, Boris; Foing, Bernard; Neukum, Gerhard

    2010-06-01

    Gusev Crater lies within the Aeolis Quadrangle of Mars at the boundary between the northern lowlands and southern highlands. The ancient valley Ma'adim Vallis dissects the highlands south of Gusev Crater and is thought to have fed the crater with sediments. High Resolution Stereo Camera data and Digital Elevation Models were used to construct a geologic-geomorphic map (173.5-178.5° E, 10-18° S) and cross-sections, complemented by data from Mars Orbiter Camera, Mars Orbiter Laser Altimeter and Thermal Emission Imaging System. Three geologic domains are recognised: the highlands in the south, Gusev Crater and lowlands in the north. Twelve units are mapped, with thicknesses ranging from hundred meters to several kilometres. Thicknesses of units, and their bedding attitude, are estimated combining the geologic map and topographic information. Relative ages are determined from crater counts, ranging from Early Noachian for highland units to Middle Amazonian for units in Gusev Crater and in lowlands. Episodes of intense geologic activity (deposition, volcanism, deformation) occur at around 4.0 Ga, 3.7 Ga, and 3.5 Ga. Comparing the geometry of the Gusev Crater with similar sized, filled and un-filled, Martian craters, suggests that the Columbia Hills are relics of the original central peak of Gusev Crater.

  7. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  8. Studying the TEM response of a 3-D conductor at a geological contact using the FDTD method

    SciTech Connect

    Wang, T.; Tripp, A.C.; Hohmann, G.W.

    1995-07-01

    Many mineral targets are located near contact zones. Since the change of resistivity across the contact can distort or obscure the transient electromagnetic (TEM) response of the target, it is important to understand the possible effects. Previous investigators have examined similar problems using scale models. For example, Spies and Parker (1984) studied the TEM responses of fixed-loop and moving-loop configurations to geological contacts with lateral resistivity variations. More recently, Wilt (1991) systematically studied TEM soundings near a geological contact and observed that different survey systems respond to the contact in different ways. This paper will illustrate the use of the finite-difference, time-domain (FDTD) algorithm of Wang and Hohmann (1993) for calculating the TEM response of a 3-D conductive body at a geological contact. The algorithm is based on the Yee staggered grid FDTD method for solving the transient electrical nonmagnetic field responses of a 3-D model. On a suitable computer, a wide range of model responses can be readily calculated, a versatility that scale modeling does not share. This study uses a fixed transmitter loop, roving-receiver configuration. Many other configurations can be regarded as special cases of this survey. It is commonly employed, for instance, by the Newmont EMP (Body and Wiles, 1984), UTEM (West et al., 1984), and Geonics EM37 systems. The configuration also facilitates finite-difference, time-domain modeling because it does not require frequent movement of the source.

  9. Simulating Seismic Wave Propagation in 3-D Structure: A Case Study For Istanbul City

    NASA Astrophysics Data System (ADS)

    Yelkenci, Seda; Aktar, Mustafa

    2013-04-01

    Investigation of the wave propagation around the Marmara Sea, in particular for the city of Istanbul is critical because this target area is identified as one of the megacities with the highest seismic risk in the world. This study makes an attempt for creating an integrated 3D seismic/geologic model and precise understanding of 3-D wave propagation in the city of Istanbul. The approach is based on generating synthetic seismograms using realistic velocity structures as well as accurate location, focal mechanism and source parameters of reference earthquakes. The modarate size reference earthquakes occured in the Marmara Sea and were recorded by the National Seismic Network of Turkey as well as the network of Istanbul Early Warning and Rapid Response System. The seismograms are simulated by means of a 3-D finite difference method operated on parallel processing environment. In the content of creating a robust velocity model; 1D velocity models which are derived fom previous crustal studies of Marmara region such as refraction seismic and receiver functions have been conducted firstly for depths greater than 1km. Velocity structure in shallower part of the study region is then derived from recent geophysical and geotechnical surveys. To construct 3-D model from the obtained 1-D model data, a variety of interpolation methods are considered. According to the observations on amplitude and arrival time based on comparison of simulated seismograms, the considered velocity model is refined the way that S delay times are compensated. Another important task of this work is an application of the finite difference method to estimate three-dimensional seismic responses for a specified basin structure including soft sediments with low shear velocities in respect of the surrounded area in the Asian part of Istanbul. The analysis performed both in the time and frequency domain, helps in understanding of the comprehensive wave propagation characteristics and the distribution of

  10. Shallow subsurface control on earthquake damage patterns: first results from a 3D geological voxel model study (Tokyo Lowland, Japan)

    NASA Astrophysics Data System (ADS)

    Stafleu, Jan; Busschers, Freek; Tanabe, Susumu

    2016-04-01

    The Tokyo Lowland is situated in a Neogene sedimentary basin near the triple junction of the North American, Pacific, and Philippine tectonic plates. The basin is filled with Neogene and Quaternary sediments up to a thickness of 3 km. In the upper 70 m of the basin, thick sequences of soft Holocene sediments occur which are assumed to have played a key role in the spatial variation of damage intensity during the 1923 Kanto earthquake (Magnitude 7.9 to 8.3). Historical records show this earthquake destroyed large parts of the Tokyo urban area which in that time was largely made up by wooden houses. Although the epicentre was 70 km to the southwest of Tokyo, severe damage occurred north of the city centre, presumably due to ground motion amplification in the soft Holocene sediments in the shallow subsurface. In order to assess the presumed relation between the damage pattern of the 1923 earthquake and the occurrence of soft Holocene sediments in the shallow subsurface, we constructed a 3D geological voxel model of the central part of the Tokyo Lowland. The model was constructed using a methodology originally developed for the lowlands of the Netherlands. The modelling workflow basically consists of three steps. First, some 10,000 borehole descriptions (gathered for geomechanical purposes), were subdivided into geological units that have uniform sediment characteristics, using both lithological and geomechanical (N-value) criteria. Second, 2D bounding surfaces were constructed, representing tops and bases of the geological units. These surfaces were used to place each voxel (100 by 100 by 1 m) within the correct geological unit. The N-values and lithological units in the borehole descriptions were subsequently used to perform a 3D stochastic interpolation of N-value and lithological class within each geological unit. Using a vertical voxel stack analysis, we were able to create a map showing the accumulated thickness of soft muds in the Holocene succession. A

  11. 3D Reconstruction of virtual colon structures from colonoscopy images.

    PubMed

    Hong, DongHo; Tavanapong, Wallapak; Wong, Johnny; Oh, JungHwan; de Groen, Piet C

    2014-01-01

    This paper presents the first fully automated reconstruction technique of 3D virtual colon segments from individual colonoscopy images. It is the basis of new software applications that may offer great benefits for improving quality of care for colonoscopy patients. For example, a 3D map of the areas inspected and uninspected during colonoscopy can be shown on request of the endoscopist during the procedure. The endoscopist may revisit the suggested uninspected areas to reduce the chance of missing polyps that reside in these areas. The percentage of the colon surface seen by the endoscopist can be used as a coarse objective indicator of the quality of the procedure. The derived virtual colon models can be stored for post-procedure training of new endoscopists to teach navigation techniques that result in a higher level of procedure quality. Our technique does not require a prior CT scan of the colon or any global positioning device. Our experiments on endoscopy images of an Olympus synthetic colon model reveal encouraging results with small average reconstruction errors (4.1 mm for the fold depths and 12.1 mm for the fold circumferences). PMID:24225230

  12. Influence of pre-existing salt structures in the 3D pattern of multilayer folding

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris J. P.; Collignon, Marine

    2014-05-01

    Upward movement of the Precambrian Hormuz salt in the Fars region of the Zagros is supposed to have started as early as Late Cretaceous. The Late Cretaceous - Tertiary deformation events that lead to the folding of the sedimentary cover in this area would have therefore, enhance the upward salt movement by squeezing the pre-existing salt structures. How these salt diapirs evolve under such compressive events has already been previously addressed using analogue models (e.g. Callot et al. 2012). The same authors observed that pre-existing salt structures control the size and geometry of folds in sandbox models. Our previous work has shown that 3D folding instability gives rise to a wide variety of fold shapes (e.g. from dome shape structures to long en echelon or straight anticlines), resulting of the interactions between growing fold segments. The three dimensional growth of these folds, the wavelength and the lateral propagation, is itself controlled by physical parameters. However, the existence of initial weak zones such as pre-existing salt plugs within the sedimentary cover can affect the development of such folds by localizing part of the deformation. In this study we have used numerical modeling to investigate how the fold pattern in 3D multilayer folding is affected by pre-existing salt structures. High-resolution 3D folding simulations (with and without pre-existing salt structures) were performed with the parallel code LaMEM. Cylindrically shaped diapirs with different diameters and heights have been added to a multilayer folding setup. The use of a finite element based landscape evolution model (both erosion and sedimentation) allows for initially buried salt diapirs to be exposed at the surface during folding evolution. Acknowledgements Funding was provided by the European Research Council under the European Community's Seventh Framework program (FP7/2007-2013) ERC Grant agreement #258830. 3D simulations are performed in the IBM Blue Gene/Q JUQUEEN

  13. Sustainable growth in America's heartland; 3-D geologic maps as the foundation

    USGS Publications Warehouse

    Central Great Lakes Geologic Mapping Coalition; Illinois State Geological Survey; Indiana Geological Survey; Michigan Geological Survey Division; Ohio Division of Geological Survey; U.S. Geological Survey

    1999-01-01

    The central Great Lakes states of Illinois, Indiana, Michigan, and Ohio constitute one of the most productive and economically important regions in the country--America's heartland. The agriculture, industry, business, recreation, and ecology of these states are based on a common geologic heritage. During the last 1.8 million years, glaciers repeatedly advanced and retreated across the region, leaving behind a thick, complex blanket of intermixed layers of mud, clay, silt, sand, and gravel. Decisionmakers need knowledge of the glacial deposits--their characteristics, three-dimensional distribution, and thickness. To provide this knowledge, a coalition of state and federal geological surveys has formed to conduct the necessary studies in these four states to depict the three-dimensional nature of these glacial deposits and to interpret these data in cooperation with the user community for specific societal needs.

  14. Visualization of three dimensional earth fissures in geological structure

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Yu, J.; Liu, Y.; Gong, H.; Chen, Y.; Chen, B.

    2015-11-01

    This paper proposes a new method for visualizing the earth fissures of geological structure in three dimensional (3-D) domains on the basis of the seismic data and features information of earth fissures. The seismic data were interpreted for obtaining the stratagraphic data with various lithological information and the depth of the earth fissures. The spatial distribution of the ground fissures including the dip, strike and width were digitalized on an ArcGIS platform. Firstly, the 3-D geological structure was rebuilt using the Generalized Tri-Prism (GTP) method which is a real solid method for displaying geological structures. The GTP method can reflect the inner material of the strata and can simulate complicated geological structures such as faults and stratagraphic pinch outs. The upper and lower surfaces of each stratum consist of Triangle Irregular Networks (TIN). The inner solid between the two surfaces are a series of triangular prisms. Secondly, since the width of the ground fissure gradually decreases with depth, multiple edge lines of the earth fissures on the bottom stratum surface are deduced on the basis of the fissure characteristics. Then, the model of the earth fissures consisting of a series of triangular pyramids can be constructed using these points and the edge lines. A cutting operation was carried out on the 3-D geological structure using this ground fissures model. If the surfaces of the ground fissures model intersects with the GTPs in the geological structure model, new GTPs were generated within the local regions. During this process, the topological relations between TIN, triangular prism and lines were reconstructed so that the visualization of ground fissures in the geological structure model is realized. This method can facilitate the mechanism for studying fissures and avoid the gaps between the fissure solid and the geological structure to accurately reflect their 3-D characteristics.

  15. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    On page 3712, E. Fantino, A. Chiappone, and co-workers fabricate conductive 3D hybrid structures by coupling the photo-reduction of metal precursors with 3D printing technology. The generated structures consist of metal nanoparticles embedded in a polymer matrix shaped into complex multilayered architectures. 3D conductive structures are fabricated with a digital light-processing printer incorporating silver salt into photocurable formulations. PMID:27167030

  16. Digital Geology from field to 3D modelling and Google Earth virtual environment: methods and goals from the Furlo Gorge (Northern Apennines - Italy)

    NASA Astrophysics Data System (ADS)

    De Donatis, Mauro; Susini, Sara

    2014-05-01

    A new map of the Furlo Gorge was surveyed and elaborated in a digital way. In every step of work we used digital tools as mobile GIS and 3D modelling software. Phase 1st Starting in the lab, planning the field project development, base cartography, forms and data base were designed in the way we thought was the best for collecting and store data in order of producing a digital n­-dimensional map. Bedding attitudes, outcrops sketches and description, stratigraphic logs, structural features and other informations were collected and organised in a structured database using rugged tablet PC, GPS receiver, digital cameras and later also an Android smartphone with some survey apps in-­house developed. A new mobile GIS (BeeGIS) was developed starting from an open source GIS (uDig): a number of tools like GPS connection, pen drawing annotations, geonotes, fieldbook, photo synchronization and geotagging were originally designed. Phase 2nd After some month of digital field work, all the informations were elaborated for drawing a geologic map in GIS environment. For that we use both commercial (ArcGIS) and open source (gvSig, QGIS, uDig) without big technical problems. Phase 3rd When we get to the step of building a 3D model (using 3DMove), passing trough the assisted drawing of cross-­sections (2DMove), we discovered a number of problems in the interpretation of geological structures (thrusts, normal faults) and more in the interpretation of stratigraphic thickness and boundaries and their relationships with topography. Phase 4th Before an "on­-armchair" redrawing of map, we decide to go back to the field and check directly what was wrong. Two main vantages came from this: (1) the mistakes we found could be reinterpreted and corrected directly in the field having all digital tools we need; (2) previous interpretations could be stored in GIS layers keeping memory of the previous work (also mistakes). Phase 5th A 3D model built with 3D Move is already almost self

  17. 3d-modelling workflows for trans-nationally shared geological models - first approaches from the project GeoMol

    NASA Astrophysics Data System (ADS)

    Rupf, Isabel

    2013-04-01

    To meet the EU's ambitious targets for carbon emission reduction, renewable energy production has to be strongly upgraded and made more efficient for grid energy storage. Alpine Foreland Basins feature a unique geological inventory which can contribute substantially to tackle these challenges. They offer a geothermal potential and storage capacity for compressed air, as well as space for underground storage of CO2. Exploiting these natural subsurface resources will strongly compete with existing oil and gas claims and groundwater issues. The project GeoMol will provide consistent 3-dimensional subsurface information about the Alpine Foreland Basins based on a holistic and transnational approach. Core of the project GeoMol is a geological framework model for the entire Northern Molasse Basin, complemented by five detailed models in pilot areas, also in the Po Basin, which are dedicated to specific questions of subsurface use. The models will consist of up to 13 litho-stratigraphic horizons ranging from the Cenozoic basin fill down to Mesozoic and late Paleozoic sedimentary rocks and the crystalline basement. More than 5000 wells and 28 000 km seismic lines serve as input data sets for the geological subsurface model. The data have multiple sources and various acquisition dates, and their interpretations have gone through several paradigm changes. Therefore, it is necessary to standardize the data with regards to technical parameters and content prior to further analysis (cf. Capar et al. 2013, EGU2013-5349). Each partner will build its own geological subsurface model with different software solutions for seismic interpretation and 3d-modelling. Therefore, 3d-modelling follows different software- and partner-specific workflows. One of the main challenges of the project is to ensure a seamlessly fitting framework model. It is necessary to define several milestones for cross border checks during the whole modelling process. Hence, the main input data set of the

  18. Image quality improvement for a 3D structure exhibiting multiple 2D patterns and its implementation.

    PubMed

    Hirayama, Ryuji; Nakayama, Hirotaka; Shiraki, Atsushi; Kakue, Takashi; Shimobaba, Tomoyoshi; Ito, Tomoyoshi

    2016-04-01

    A three-dimensional (3D) structure designed by our proposed algorithm can simultaneously exhibit multiple two-dimensional patterns. The 3D structure provides multiple patterns having directional characteristics by distributing the effects of the artefacts. In this study, we proposed an iterative algorithm to improve the image quality of the exhibited patterns and have verified the effectiveness of the proposed algorithm using numerical simulations. Moreover, we fabricated different 3D glass structures (an octagonal prism, a cube and a sphere) using the proposed algorithm. All 3D structures exhibit four patterns, and different patterns can be observed depending on the viewing direction. PMID:27137021

  19. X-Ray Nanofocus CT: Visualising Of Internal 3D-Structures With Submicrometer Resolution

    NASA Astrophysics Data System (ADS)

    Weinekoetter, Christian

    2008-09-01

    High-resolution X-ray Computed Tomography (CT) allows the visualization and failure analysis of the internal micro structure of objects—even if they have complicated 3D-structures where 2D X-ray microscopy would give unclear information. During the past several years, computed tomography has progressed to higher resolution and quicker reconstruction of the 3D-volume. Most recently it even allows a three-dimensional look into the inside of materials with submicron resolution. With the use of nanofocus® tube technology, nanoCT®-systems are pushing forward into application fields that were exclusive to high cost and rare available synchrotron techniques. The study was performed with the new nanotom, a very compact laboratory system which allows the analysis of samples up to 120 mm in diameter and weighing up to 1 kg with exceptional voxel-resolution down to <500 nm (<0.5 microns). It is the first 180 kV nanofocus® computed tomography system in the world which is tailored specifically to the highest-resolution applications in the fields of material science, micro electronics, geology and biology. Therefore it is particularly suitable for nanoCT-examinations e.g. of synthetic materials, metals, ceramics, composite materials, mineral and organic samples. There are a few physical effects influencing the CT quality, such as beam-hardening within the sample or ring-artefacts, which can not be completely avoided. To optimize the quality of high resolution 3D volumes, the nanotom® includes a variety of effective software tools to reduce ring-artefacts and correct beam hardenings or drift effects which occurred during data acquisition. The resulting CT volume data set can be displayed in various ways, for example by virtual slicing and sectional views in any direction of the volume. By the fact that this requires only a mouse click, this technique will substitute destructive mechanical slicing and cutting in many applications. The initial CT results obtained with the

  20. D Geological Outcrop Characterization: Automatic Detection of 3d Planes (azimuth and Dip) Using LiDAR Point Clouds

    NASA Astrophysics Data System (ADS)

    Anders, K.; Hämmerle, M.; Miernik, G.; Drews, T.; Escalona, A.; Townsend, C.; Höfle, B.

    2016-06-01

    Terrestrial laser scanning constitutes a powerful method in spatial information data acquisition and allows for geological outcrops to be captured with high resolution and accuracy. A crucial aspect for numerous geologic applications is the extraction of rock surface orientations from the data. This paper focuses on the detection of planes in rock surface data by applying a segmentation algorithm directly to a 3D point cloud. Its performance is assessed considering (1) reduced spatial resolution of data and (2) smoothing in the course of data pre-processing. The methodology is tested on simulations of progressively reduced spatial resolution defined by varying point cloud density. Smoothing of the point cloud data is implemented by modifying the neighborhood criteria during normals estima-tion. The considerable alteration of resulting planes emphasizes the influence of smoothing on the plane detection prior to the actual segmentation. Therefore, the parameter needs to be set in accordance with individual purposes and respective scales of studies. Fur-thermore, it is concluded that the quality of segmentation results does not decline even when the data volume is significantly reduced down to 10%. The azimuth and dip values of individual segments are determined for planes fit to the points belonging to one segment. Based on these results, azimuth and dip as well as strike character of the surface planes in the outcrop are assessed. Thereby, this paper contributes to a fully automatic and straightforward workflow for a comprehensive geometric description of outcrops in 3D.

  1. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

    Fantino, Erika; Chiappone, Annalisa; Roppolo, Ignazio; Manfredi, Diego; Bongiovanni, Roberta; Pirri, Candido Fabrizio; Calignano, Flaviana

    2016-05-01

    Coupling the photoreduction of a metal precursor with 3D-printing technology is shown to allow the fabrication of conductive 3D hybrid structures consisting of metal nanoparticles and organic polymers shaped in complex multilayered architectures. 3D conductive structures are fabricated incorporating silver nitrate into a photocurable oligomer in the presence of suitable photoinitiators and exposing them to a digital light system. PMID:26992060

  2. Impact Craters on Mars: Natural 3D Exploration Probes of Geological Evolution

    NASA Technical Reports Server (NTRS)

    Garvin, James B.

    2005-01-01

    Introduction: The population of impact craters preserved on the surface of Mars offers fundamental constraints on the three- dimensional mechanical characteristics of the martian crust, its volatile abundance, and on the styles of erosion that have operated during essentially all epochs of martian geological history. On the basis of the present- day wealth of morphologic and geometric observations of impact landforms on Mars [ 1-31, an emerging understanding of the three-dimensional physical properties of the martian uppermost crust in space and time is at hand. In this summary, the current basis of understanding of the relatively non- degraded population of impact landforms on Mars is reviewed, and new Mars Global Surveyor (MGS)-based (MOLA) measurements of global geometric properties are summarized in the context of upcoming observations by Mars Reconnaissance Orbiter (MRO).

  3. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

    Mattingly, William A.; Chariker, Julia H.; Paris, Richard; Chang, Dar-jen; Pani, John R.

    2015-01-01

    Branching tubular structures are prevalent in many different organic and synthetic settings. From trees and vegetation in nature, to vascular structures throughout human and animal biology, these structures are always candidates for new methods of graphical and visual expression. We present a modeling tool for the creation and interactive modification of these structures. Parameters such as thickness and position of branching structures can be modified, while geometric constraints ensure that the resulting mesh will have an accurate anatomical structure by not having inconsistent geometry. We apply this method to the creation of accurate representations of the different types of retinal cells in the human eye. This method allows a user to quickly produce anatomically accurate structures with low polygon counts that are suitable for rendering at interactive rates on commodity computers and mobile devices. PMID:27087764

  4. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

    PubMed Central

    Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli

    2009-01-01

    A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709

  5. 3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.

    NASA Astrophysics Data System (ADS)

    Al-Arifi, Nassir; El Kherpy, Sami; Koulakov, Ivan

    2014-05-01

    Abu Dabbab seismogenic source region is of unique seismic activity located on the Egyptian Red Sea coast. It's known as earthquake Cannons where the earthquakes are accompanied by a sound of distinct rumbling similar to the sound of a distant quarry blast which is heard by humans for several generations. Seismic activity of Abu Dabbab becomes very well determined after establishing of the Egyptian National Seismic Network 1997. Joint earthquake tomography inversion of local and regional data has been performed in order to image the crustal heterogeneity and the origin of the cannons earthquakes. Most previous studies suggested that this activity is of magmatic origin. We found the seismicity forms an arc shaped cluster that surrounds an aseismic block. This aseismic block has high velocities and a low Vp/Vs ratio. The origin of this seismic activity is probably due an active fault below the non-deformed block of Precambrian Igneous rock reaching a depth of ~10 km. Spatial mapping of the frequency magnitude distribution of the earthquakes and 3D-b-value indicate a strong variation moreover high b-value (1.4) at depth downward the rigid block. The Combined interpretation of the seismic imaging and 3D b-value in addition to the seismological and the geophysical observations revealed the tectonic origin of the earthquake activity in this area which is related strongly to the evolution of the crust in the Red Sea and its tectonic activity. KEYWARD:Three dimensional Crustal Structure - Seismic activity -Three-D b-value- Red Sea tectonics- Tectonic activity

  6. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and 3-dimensional structural information

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

    SUMMARY Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of 3-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  7. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at http://prodata.swmed.edu/PROMALS3D. PMID:24170408

  8. The crustal and mantle velocity structure in central Asia from 3D traveltime tomography

    NASA Astrophysics Data System (ADS)

    Sun, Y.; Martin, R. V.; Toksoz, M. N.; Pei, S.

    2010-12-01

    The lithospheric structure in central Asia features large blocks such as the Indian plate, the Afghan block, the Turan plate, and the Tarim block. This geologically and tectonically complicated area is also one of the most seismically active regions in the world. We developed P- and S- wave velocity structures of the central Asia in the crust using the traveltime data from Kyrgyzstan, Tajikistan, Kazakhstan, and Uzbek. We chose the events and stations between 32N65E and 45N85E and focused on the areas of Pamir and western Tianshan. In this data set, there are more than 6000 P and S arrivals received at 80 stations from about 300 events. The double difference tomography is applied to relocate events and to invert for seismic structures simultaneously. Our results provide accurate locations of earthquakes and high resolution crustal structure in this region. To extend the model deeper into the mantle through the upper mantle transition zone, ISC/EHB data for P and PP phases are combined with the ABCE data. To counteract the “smearing effect,” the crust and upper mantle velocity structure, derived from regional travel-times, is used. An adaptive grid method based on ray density is used in the inversion. A P-wave velocity model extending down to a depth of 2000 km is obtained. regional-teleseismic tomography provides a high-resolution, 3-D P-wave velocity model for the crust, upper mantle, and the transition zone. The crustal models correlate well with geologic and tectonic features. The upper mantle tomograms show the images of Tian Shan. The slab geometry is quite complex, reflecting the history of the changes in the plate motions and collision processes. Vp/Vs tomography was also determined in the study region, and an attenuation tomography was obtained as well.

  9. GMOL: An Interactive Tool for 3D Genome Structure Visualization.

    PubMed

    Nowotny, Jackson; Wells, Avery; Oluwadare, Oluwatosin; Xu, Lingfei; Cao, Renzhi; Trieu, Tuan; He, Chenfeng; Cheng, Jianlin

    2016-01-01

    It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function. PMID:26868282

  10. Characterizing 3D RNA structure by single molecule FRET.

    PubMed

    Stephenson, James D; Kenyon, Julia C; Symmons, Martyn F; Lever, Andrew M L

    2016-07-01

    The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model. PMID:26853327

  11. SAFAS: Unifying Form and Structure through Interactive 3D Simulation

    ERIC Educational Resources Information Center

    Polys, Nicholas F.; Bacim, Felipe; Setareh, Mehdi; Jones, Brett D.

    2015-01-01

    There has been a significant gap between the tools used for the design of a building's architectural form and those that evaluate the structural physics of that form. Seeking to bring the perspectives of visual design and structural engineering closer together, we developed and evaluated a design tool for students and practitioners to explore the…

  12. Determining 3-D motion and structure from image sequences

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

    A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.

  13. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

    We review the observational evidences concerning the three-dimensional structure of the Galactic bulge. Although the inner few kpc of our Galaxy are normally referred to as the bulge, all the observations demonstrate that this region is dominated by a bar, i.e., the bulge is a bar. The bar has a boxy/peanut (X-shaped) structure in its outer regions, while it seems to become less and less elongated in its innermost region. A thinner and longer structure departing from the main bar has also been found, although the observational evidences that support the scenario of two separate structures has been recently challenged. Metal-poor stars ([Fe/H] ≲ -0.5 dex) trace a different structure, and also have different kinematics.

  14. The Deep Structure of the South Atlantic Kwanza Basin - Insights from 3D Structural and Gravimetric modelling

    NASA Astrophysics Data System (ADS)

    Nicolai, Christina V.; Scheck-Wenderoth, Magdalena; Warsitzka, Michael

    2010-05-01

    Three dimensional geological models constrained by potential field data have proven to be powerful tools for the investigation of areas where conventional seismic surveying fails to deliver satisfactory results. Especially in basins containing thick sedimentary and/or evaporite layers, the detection of crustal structures such as synrift halfgrabens or basement highs is considerably enhanced by potential field data. Knowledge on the distribution and configuration of crustal structures is inalienable for the reconstruction of the tectonic history of a continental margin. In this study, we present results from 3D gravimetric modelling of the Kwanza Basin offshore Angola accomplished to investigate the formation of the basin in response to the opening of the South Atlantic. Although the post-rift evolution of the Kwanza Basin is well studied, little is known about the basins early history. This is mainly due to the missing knowledge of its crustal structure owing to the masking effect of an up to 3 km thick salt layer, which seismically obscures the underlying basement. To get an insight into the deeper structure of the Angolan margin we combined 3D structural, isostatic and gravimetric modelling. 2D seismic reflection data was used to determine the structural setting and the configuration of the stratigraphic units in the sedimentary part of the basin, whereas its crustal structure was constrained by isostatic and gravity modelling. The resulting geological model confirms and extends previous observations, and adds new details to the hitherto dim picture of the Kwanza Basins crustal architecture. In addition, it raises new questions on the volcanic or non-volcanic origin of the margin, and the potential of transfer faults to dissect the latter into independently evolving tectonic segments.

  15. A crust-scale 3D structural model of the Beaufort-Mackenzie Basin (Arctic Canada)

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Scheck-Wenderoth, Magdalena; Lewerenz, Björn; Kroeger, Karsten Friedrich

    2013-04-01

    The Beaufort-Mackenzie Basin was initiated in the Early Jurassic as part of an Arctic rifted passive continental margin which soon after became overprinted by Cordilleran foreland tectonics. Decades of industrial exploration and scientific research in this petroliferous region have produced a wide spectrum of geological and geophysical data as well as geoscientific knowledge. We have integrated available grids of sedimentary horizons, well data, seismic reflection and refraction data, and the observed regional gravity field into the first crust-scale 3D structural model of the Beaufort-Mackenzie Basin. Many characteristics of this model reflect the complex geodynamic and tectonostratigraphic history of the basin. The Mesozoic-Cenozoic sedimentary part of the model comprises seven clastic units (predominantly sandy shales) of which the modelled thickness distributions allow to retrace the well-established history of the basin comprising a gradual north(east)ward shift of the main depocentres as well as diverse phases of localised erosion. As a result of this development, the present-day configuration of the basin reveals that the sedimentary units tend to be younger, more porous, and thus less dense towards the north at a constant depth level. By integrating three refraction seismic profiles and performing combined isostatic and 3D gravity modelling, we have modelled the sub-sedimentary basement of the Beaufort-Mackenzie Basin. The continental basement spans from unstretched domains (as thick as about 42 km) in the south to extremely thinned domains (of less than 5 km thickness) in the north where it probably represents transitional crust attached to the oceanic crust of the Canada Basin. The uppermost parts of the continental crust are less dense (ρ = 2710 kg/m3) and most probably made up by pre-Mesozoic meta-sediments overlying a heavier igneous and metamorphic crust (ρ = 2850 kg/m3). The presented crust-scale 3D structural model shows that the greatest

  16. Gravimetric 3D Subsurface Modelling of the Cerro Do Jarau Structure, Rio Grande Do Sul, Brazil.

    NASA Astrophysics Data System (ADS)

    Giacomini, B. B.

    2014-12-01

    Although common in other bodies of the solar system, impact craters formed in basaltic terrains are rare on Earth and only a few examples are known. Two of these craters are located south of Brazil, the Vargeão and Vista Alegre impact craters. The Cerro do Jarau structure is not confirmed, but is a possible third Brazilian basaltic crater, formed above the Serra Geral basalt floods of the Paraná Basin like the other two. Cerro do Jarau is a 13 km circular landform that rises over 200 meters above the plains of the "pampas" in southern Brazil. The name, meaning "Jarau hills", is given after the crests of silicified and deformed Botucatu sandstones, which form a semiring of elevated hills in the northern part of the structure. This work focused on the construction of a 3D subsurface geological model that could explain a new set of ground gravimetric data. Bouguer anomalies were calculated from gravity acceleration measured at 313 stations irregularly distributed on the area of the impact structure. A regional component represented by a polynomial trend surface was extracted from the total Bouguer anomalies. The residual Bouguer map (fig. 1) shows a strong positive anomaly with a NE-SW trend, located in the northeastern part of the structure. This gravity feature is not common in other impact structures, being possibly related to a dike intrusion. However, the negative anomaly present in the center of the structure and the circular positive anomaly surrounding the central part of the structure could be related to an impact structure. The positive circular anomaly is not spatially coincident with the edges of the structure, a feature that is also observed at the Vargeão and Vista Alegre impact structures. Density values of basalts, sandstones and breccias were measured from rock samples and each average value were used as constraints for the 3D model developed with the Geosoft® VOXI Earth modelling.This model provided a better understanding of the subsurface design

  17. 3D Thermoelectric Structures Derived from a New Mixed Micromachining Process

    NASA Astrophysics Data System (ADS)

    Du, Chen-Hsun; Lee, Chengkuo

    2000-12-01

    This paper proposes an innovative 3D thermoelectric structure which significantly reduce the componet size without deterioration of sensor performance. Based on complementary metal-oxide-semiconductor (CMOS) transistor compatible process, this 3D thermoelectric structure is demonstrated and fabricated by combining front-side silicon anisotropic wet etching and aluminum sacrificial layer etching technique. The voltage responsivity of derived 3D thermoelectric structure with 180× 180 μm2 pixel size can be as high as 190 V/W in vacuum. This new thermoelectric structure shows its potential to be an excellent pixel structure of infrared sensor array for infrared recognition applications.

  18. LV motion tracking from 3D echocardiography using textural and structural information.

    PubMed

    Myronenko, Andriy; Song, Xubo; Sahn, David J

    2007-01-01

    Automated motion reconstruction of the left ventricle (LV) from 3D echocardiography provides insight into myocardium architecture and function. Low image quality and artifacts make 3D ultrasound image processing a challenging problem. We introduce a LV tracking method, which combines textural and structural information to overcome the image quality limitations. Our method automatically reconstructs the motion of the LV contour (endocardium and epicardium) from a sequence of 3D ultrasound images. PMID:18044597

  19. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  20. Internal Structure of Periglacial Landforms: Assessment using 3D Electrical Resistivity Imaging (ERI)

    NASA Astrophysics Data System (ADS)

    Emmert, Adrian; Kneisel, Christof

    2015-04-01

    The occurrence of internal heterogeneities within periglacial landforms (e.g. frost table topography or varying ice content) is in most cases not inferable from the surface. Hence, to develop an enhanced understanding of the interaction between surface and subsurface processes, it is necessary to analyse the internal structure of different periglacial landforms and landform elements. The assessment of the internal structure is provided by the application of three-dimensional Electrical Resistivity Imaging (ERI). ERI is the technique of merging datum points from several parallel and perpendicular performed two-dimensional ERT (Electrical Resistivity Tomography) measurements and inverting the data set with a 3D inversion algorithm (sometimes also referred to as quasi-3D ERT). The application of this method has proven to be a valuable tool for mapping the spatial extent of isolated permafrost bodies and associated subsurface conditions. In this contribution, we present results from four ERI measurements, carried out in summer 2014 at different investigation sites in the Swiss Alps: Three measurements were performed on pebbly rockglaciers of different size and topographical position and one measurement was performed on a solifluction slope. Each of the 3D survey grids consists of 17 to 32 single 2D ERT surveys (Dipol-Dipol or Wenner-Schlumberger array) and covers an area of between 6000 m² and 7000 m², depending on the specific survey grid set-up. The inversions of the data sets were performed using the two different inversion algorithms of the software products "RES3DINV" and "BERT" (Boundless Electrical Resistivity Tomography) for a comparative analysis and to further support the geomorphological interpretation of the geophysical models. Each of the resulting resistivity models shows strong small-scale spatial heterogeneities between the investigated landforms but also within landform elements. For the investigated rockglacier sites, these structures include

  1. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

    PubMed

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  2. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side.

  3. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III–V, and II–VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain–low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  4. Topologic connection between 2-D layered structures and 3-D diamond structures for conventional semiconductors.

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

    When coming to identify new 2D materials, our intuition would suggest us to look from layered instead of 3D materials. However, since graphite can be hypothetically derived from diamond by stretching it along its [111] axis, many 3D materials can also potentially be explored as new candidates for 2D materials. Using a density functional theory, we perform a systematic study over the common Group IV, III-V, and II-VI semiconductors along different deformation paths to reveal new structures that are topologically connected to but distinctly different from the 3D parent structure. Specifically, we explore two major phase transition paths, originating respectively from wurtzite and NiAs structure, by applying compressive and tensile strain along the symmetry axis, and calculating the total energy changes to search for potential metastable states, as well as phonon spectra to examine the structural stability. Each path is found to further split into two branches under tensile strain-low buckled and high buckled structures, which respectively lead to a low and high buckled monolayer structure. Most promising new layered or planar structures identified include BeO, GaN, and ZnO on the tensile strain side, Ge, Si, and GaP on the compressive strain side. PMID:27090430

  5. Pushing the Limits of Geological Mapping Outside the Earth: 3D Modeling of Strike-Slip and Extensional Fault Systems in Meridiani Planum Region, Mars.

    NASA Astrophysics Data System (ADS)

    Vidal Royo, O.

    2014-12-01

    GIS and geological modeling software have radically changed the means by which geological mapping is produced, published and visualized. This type of software environment normally requires a spatially aware reference system to position data and interpretation, often referred as georeferenced data (i.e. geographic data referenced on the Earth). However, for this study we coin the term areoreferenced data (i.e. Mars-referenced "geographic" data). Thanks to the wealth of areoreferenced data made available by the NASA and the HiRise at University of Arizona it is now possible to carry out 3D areographic and areologic (i.e. related to the topography and geology of Mars, respectively) reconstructions in great detail. The present work benefits from the availability of software and areographic data, and presents the results of an areologic map and 3D model of the fault systems in the Meridiani Planum of Mars. The work has been carried out in Move™ (developed by Midland Valley Exploration), a geological modeling toolkit that allows for easy data loading in a wide range of formats as well as straightforward 2D/3D model building tools of geological bodies. Initial data consisted of Digital Terrain Model and orthoimages (NASA/JPL/University of Arizona/USGS). From these we have interpreted several structural domains: right-lateral strike-slip systems with associated releasing bends, which gave room to an extensional event causing a horizontal-axis rotation of the bedding. Bedding ranges from subhorizontal in the southern domain where strike-slip prevails to nearly 40º in the central and northern domains, where a more complex interaction between strike-slip and extensional faults is described. The stratigraphic sequence is mainly composed by moderately rounded well laminated basaltic sandstones (Squyres et al., 2004) in which a high component of sulfurs (e.g. sulfate anhydrate, hexahydrite, epsomite, gypsum) and salts (e.g. halite) has been described (Squyres et al., 2004

  6. Precision and Accuracy Parameters in Structured Light 3-D Scanning

    NASA Astrophysics Data System (ADS)

    Eiríksson, E. R.; Wilm, J.; Pedersen, D. B.; Aanæs, H.

    2016-04-01

    Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.

  7. ProSAT+: visualizing sequence annotations on 3D structure.

    PubMed

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  8. Code System for Analysis of 3-D Reinforced Concrete Structures.

    1999-11-22

    Version 00 NONSAP-C is a finite element program for determining the static and dynamic response of three-dimensional reinforced concrete structures. Long-term, or creep, behavior of concrete structures can also be analyzed. Nonlinear constitutive relations for concrete under short-term loads are incorporated in two time-independent models, a variable-modulus approach with orthotropic behavior induced in the concrete due to the development of different tangent moduli in different directions and an elastic-plastic model in which the concrete ismore » assumed to be a continuous, isotropic, and linearly elastic-plastic strain-hardening-fracture material. A viscoelastic constitutive model for long-term thermal creep of concrete is included. Three-dimensional finite elements available in NONSAP-C include a truss element, a multinode tendon element for prestressed and post tensioned concrete structures, an elastic-plastic membrane element to represent the behavior of cavity liners, and a general isoparametric element with a variable number of nodes for analysis of solids and thick shells.« less

  9. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

    Roddy, P. A.; Huang, C. Y.; Lyke, J.; Baur, J.; Durstock, M.; MacDonald, E.

    2013-12-01

    Three-dimensional printing, more formally Additive Manufacturing (AM), is being explored by groups worldwide for use in space missions, but we recognize the amazing potential of this emerging technology to produce space weather environmental sensors at costs commensurate with declining research budgets. We present here a plan to go substantially beyond the novelty stage of this technology by developing a foundation for using AM in high-assurance space system missions. Our two-pronged approach involves (1) a disciplined investigation of material properties and reliability (electrical, mechanical, radiation) of AM and (2) the extension of this knowledge to make complex structures that can exploit the advantages of AM. We address the design, manufacture, and optimization of multifunctional space structures using multi-physics design methods, integrated computational models, and AM. Integrated multifunctional structures have significant advantage in flexibility, size, weight, and power in comparison to formally attached elements, but their design and fabrication can be complex. The complexity and range in element shape, processing method, material properties and vehicle integration make this an ideal problem to advance the current state of the art methods for multiphysics mechanism design and strengthening AM processing science.

  10. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

    Li, Like; Shum, Henry; Shklyaev, Oleg; Yashin, Victor; Balazs, Anna

    Self-assembly of complex, three-dimensional structures is commonly achieved by biological cells but difficult to realize in synthetic systems with micron-scale or larger components. Some previous modeling studies have considered only the planar self-assembly of microcapsules on a substrate. In this work, nanoparticles released from the capsules bind to the substrate and to the shells of nearby capsules. The non-uniform nanoparticle deposition on a capsule's surface leads to adhesion gradients, which drive the capsules to effectively ``climb'' on top of one another and self-organize in the vertical direction. We determine conditions that favor this structural organization. In particular, we study how the vertical structuring depends on the background fluid flow, the topography of the microcapsules and the underlying surface, the capsule-capsule interaction and that between the capsules and the substrate. The findings can provide design rules for the autonomous creation of novel nanocomposites, where the layers are formed from nanoparticle-containing and nanoparticle-decorated microcapsules.

  11. Geological 3D modeling for excavation activity in an underground marble quarry in the Apuan Alps (Italy)

    NASA Astrophysics Data System (ADS)

    Vanneschi, Claudio; Salvini, Riccardo; Massa, Giovanni; Riccucci, Silvia; Borsani, Angelo

    2014-08-01

    The three-dimensional laser scanning technique has recently become common in diverse working environments. Even in geology, where further development is needed, this technique is increasingly useful in tackling various problems such as stability investigations or geological and geotechnical monitoring. Three-dimensional laser scanning supplies detailed and complete geometrical information in short working times, as a result of the acquisition of a large number of data-points that accurately model the detected surfaces. Moreover, it is possible to combine these data with high quality photographic images so as to provide important information for geological applications, as follows. A working approach, that combines terrestrial laser scanning and traditional geological surveys, is presented. A three-dimensional model, that includes information about the geological structure in an underground quarry in the Apuan Alps, is realized. This procedure is adaptable to other geological contexts, and because of its operating speed and accuracy it is invaluable for optimal excavation, in which a proper planning of quarrying activity is vital for safety and commercial reasons.

  12. Structural 3d Monitoring Using a New Sinusoidal Fitting Adjustment

    NASA Astrophysics Data System (ADS)

    Detchev, I.; Habib, A.; Lichti, D.; El-Badry, M.

    2016-06-01

    Digital photogrammetric systems combined with image processing techniques have been used for structural monitoring purposes for more than a decade. For applications requiring sub-millimetre level precision, the use of off-the-shelf DSLR cameras is a suitable choice, especially when the low cost of the involved sensors is a priority. The disadvantage in the use of entry level DSLRs is that there is a trade-off between frame rate and burst rate - a high frame rate is either not available or it cannot be sustained long enough. This problem must be overcome when monitoring a structural element undergoing a dynamic test, where a range of loads are cycled through multiple times a second. In order to estimate deflections during such a scenario, this paper proposes a new least-squares adjustment for sinusoidal fitting. The new technique is capable of processing multiple back-to-back bursts of data within the same adjustment, which synthetically increases the de-facto temporal resolution of the system. The paper describes a beam deformation test done in a structures laboratory. The experimental results were assessed in terms of both their precision and accuracy. The new method increased the effective sampling frequency three-fold, which improved the standard deviations of the estimated parameters with up to two orders of magnitude. A residual RMSE as low as 30 μm was attained, and likewise the RMSE of the computed amplitudes between the photogrammetric system and the control laser transducers was as small as 34 μm.

  13. TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants

    PubMed Central

    Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

    2014-01-01

    The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure–activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein–ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. PMID:24930145

  14. Formation of 3D structures in a volumetric photocurable material via a holographic method

    NASA Astrophysics Data System (ADS)

    Vorzobova, N. D.; Bulgakova, V. G.; Veselov, V. O.

    2015-12-01

    The principle of forming 3D polymer structures is considered, based on the display of the 3D intensity distribution of radiation formed by a hologram in the bulk of a photocurable material. The conditions are determined for limiting the cure depth and reproducing the projected wavefront configuration.

  15. Stress Recovery and Error Estimation for 3-D Shell Structures

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

    The C1-continuous stress fields obtained from finite element analyses are in general lower- order accurate than are the corresponding displacement fields. Much effort has focussed on increasing their accuracy and/or their continuity, both for improved stress prediction and especially error estimation. A previous project developed a penalized, discrete least squares variational procedure that increases the accuracy and continuity of the stress field. The variational problem is solved by a post-processing, 'finite-element-type' analysis to recover a smooth, more accurate, C1-continuous stress field given the 'raw' finite element stresses. This analysis has been named the SEA/PDLS. The recovered stress field can be used in a posteriori error estimators, such as the Zienkiewicz-Zhu error estimator or equilibrium error estimators. The procedure was well-developed for the two-dimensional (plane) case involving low-order finite elements. It has been demonstrated that, if optimal finite element stresses are used for the post-processing, the recovered stress field is globally superconvergent. Extension of this work to three dimensional solids is straightforward. Attachment: Stress recovery and error estimation for shell structure (abstract only). A 4-node, shear-deformable flat shell element developed via explicit Kirchhoff constraints (abstract only). A novel four-node quadrilateral smoothing element for stress enhancement and error estimation (abstract only).

  16. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  17. 3D Structured Grid Generation Codes for Turbomachinery

    NASA Technical Reports Server (NTRS)

    Loellbach, James; Tsung, Fu-Lin

    1999-01-01

    This report describes the research tasks during the past year. The research was mainly in the area of computational grid generation in support of CFD analyses of turbomachinery components. In addition to the grid generation work, a numerical simulation was obtained for the flow through a centrifugal gas compressor using an unstructured Navier-Stokes solver. Other tasks involved many different turbomachinery component analyses. These analyses were performed for NASA projects or for industrial applications. The work includes both centrifugal and axial machines, single and multiple blade rows, and steady and unsteady analyses. Over the past five years, a set of structured grid generation codes were developed that allow grids to be obtained fairly quickly for the large majority of configurations we encounter. These codes do not comprise a generalized grid generation package; they are noninteractive codes specifically designed for turbomachinery blade row geometries. But because of this limited scope, the codes are small, fast, and portable, and they can be run in the batch mode on small workstations. During the past year, these programs were used to generate computational grids were modified for a wide variety of configurations. In particular, the codes or wrote supplementary codes to improve our grid generation capabilities for multiple blade row configurations. This involves generating separate grids for each blade row, and then making them match and overlap by a few grid points at their common interface so that fluid properties are communicated across the interface. Unsteady rotor/stator analyses were performed for an axial turbine, a centrifugal compressor, and a centrifugal pump. Steady-state single-blade-row analyses were made for a study of blade sweep in transonic compressors. There was also cooperation on the application of an unstructured Navier-Stokes solver for turbomachinery flow simulations. In particular, the unstructured solver was used to analyze the

  18. A 3-D fluorescence imaging system incorporating structured illumination technology

    NASA Astrophysics Data System (ADS)

    Antos, L.; Emord, P.; Luquette, B.; McGee, B.; Nguyen, D.; Phipps, A.; Phillips, D.; Helguera, M.

    2010-02-01

    A currently available 2-D high-resolution, optical molecular imaging system was modified by the addition of a structured illumination source, OptigridTM, to investigate the feasibility of providing depth resolution along the optical axis. The modification involved the insertion of the OptigridTM and a lens in the path between the light source and the image plane, as well as control and signal processing software. Projection of the OptigridTM onto the imaging surface at an angle, was resolved applying the Scheimpflug principle. The illumination system implements modulation of the light source and provides a framework for capturing depth resolved mages. The system is capable of in-focus projection of the OptigridTM at different spatial frequencies, and supports the use of different lenses. A calibration process was developed for the system to achieve consistent phase shifts of the OptigridTM. Post-processing extracted depth information using depth modulation analysis using a phantom block with fluorescent sheets at different depths. An important aspect of this effort was that it was carried out by a multidisciplinary team of engineering and science students as part of a capstone senior design program. The disciplines represented are mechanical engineering, electrical engineering and imaging science. The project was sponsored by a financial grant from New York State with equipment support from two industrial concerns. The students were provided with a basic imaging concept and charged with developing, implementing, testing and validating a feasible proof-of-concept prototype system that was returned to the originator of the concept for further evaluation and characterization.

  19. Data-fusion of high resolution X-ray CT, SEM and EDS for 3D and pseudo-3D chemical and structural characterization of sandstone.

    PubMed

    De Boever, Wesley; Derluyn, Hannelore; Van Loo, Denis; Van Hoorebeke, Luc; Cnudde, Veerle

    2015-07-01

    When dealing with the characterization of the structure and composition of natural stones, problems of representativeness and choice of analysis technique almost always occur. Since feature-sizes are typically spread over the nanometer to centimeter range, there is never one single technique that allows a rapid and complete characterization. Over the last few decades, high resolution X-ray CT (μ-CT) has become an invaluable tool for the 3D characterization of many materials, including natural stones. This technique has many important advantages, but there are also some limitations, including a tradeoff between resolution and sample size and a lack of chemical information. For geologists, this chemical information is of importance for the determination of minerals inside samples. We suggest a workflow for the complete chemical and structural characterization of a representative volume of a heterogeneous geological material. This workflow consists of combining information derived from CT scans at different spatial resolutions with information from scanning electron microscopy and energy-dispersive X-ray spectroscopy. PMID:25939085

  20. Deep structure of the Argentine margin inferred from 3D gravity and temperature modelling, Colorado Basin

    NASA Astrophysics Data System (ADS)

    Autin, J.; Scheck-Wenderoth, M.; Götze, H.-J.; Reichert, C.; Marchal, D.

    2016-04-01

    Following previous work on the Colorado Basin using a 3D crustal structural model, we now investigate the presence of lower crustal bodies at the base of the crust using 3D lithospheric gravity modelling and calculations of the conductive thermal field. Our first study highlighted two fault directions and depocentres associated with thinned crust (NW-SE in the West and NE-SW at the distal margin). Fault relative chronology argues for two periods of extension: (1) NW-SE faulting and thinning in the western Colorado Basin and (2) NE-SW faulting and thinning related to the continental breakup and formation of the NE-SW-striking volcanic margins of the Atlantic Ocean. In this study, the geometry of modelled high-density Lower Crustal Bodies (LCBs) enables the reproduction of the gravimetric field as well as of the temperature measured in wells down to 4500 m. The modelled LCBs correlate with geological observations: (1) NW-SE LCBs below the deepest depocentres in the West, (2) NE-SW LCBs below the distal margin faults and the seaward dipping reflectors. Thus the proposed poly-phased evolution of the margin could as well correspond to two emplacement phases of the LCBs. The calculated conductive thermal field fits the measured temperatures best if the thermal properties (thermal conductivity and radiogenic heat production) assigned to the LCBs correspond to either high-grade metamorphic rocks or to mafic magmatic intrusions. To explain the possible lithology of the LCBs, we propose that the two successive phases of extension are accompanied by magma supply, emplaced (1) in the thinnest crust below the older NW-SE depocentres, then (2) along the NE-SW continentward boundary of the distal margin and below the volcanic seaward dipping reflectors. The South African conjugate margin records only the second NE-SW event and we discuss hypotheses which could explain these differences between the conjugate margins.

  1. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

    Madura, T. I.; Clementel, N.; Gull, T. R.; Kruip, C. J. H.; Paardekooper, J.-P.

    2015-06-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (≳120 M⊙), highly eccentric (e ˜ 0.9) binary star system η Carinae. We demonstrate the methodology used to incorporate 3D interactive figures into a PDF (Portable Document Format) journal publication and the benefits of using 3D visualization and 3D printing as tools to analyse data from multidimensional numerical simulations. Using a consumer-grade 3D printer (MakerBot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of η Carinae's inner (r ˜ 110 au) wind-wind collision interface at multiple orbital phases. The 3D prints and visualizations reveal important, previously unknown `finger-like' structures at orbital phases shortly after periastron (φ ˜ 1.045) that protrude radially outwards from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. thin-shell, Rayleigh-Taylor) that arise at the interface between the radiatively cooled layer of dense post-shock primary-star wind and the fast (3000 km s-1), adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unrecognized physical features highlight the important role 3D printing and interactive graphics can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  2. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    NASA Astrophysics Data System (ADS)

    Babu, Sabarish; Liao, Pao-Chuan; Shin, Min C.; Tsap, Leonid V.

    2006-12-01

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell, and its state. Analysis of chromosome structure is significant in the detection of diseases, identification of chromosomal abnormalities, study of DNA structural conformation, in-depth study of chromosomal surface morphology, observation of in vivo behavior of the chromosomes over time, and in monitoring environmental gene mutations. The methodology incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  3. Sensitivity of an MT Array to 3D Structure Outside the Array Footprint

    NASA Astrophysics Data System (ADS)

    Booker, J. R.; Mackie, R. L.; Burd, A. I.; Pomposiello, M. C.; Favetto, A. B.

    2015-12-01

    Standard data collection strategy in magnetotellurics (MT) is to deploy a profile or array of sites that spans the target of interest. There is no expectation that structure can be imaged outside the area covered by sites. We have inverted two MT arrays for 3D structure under Argentina. The two arrays do not overlap, but serendipitously the 3D model for the northern array overlaps the position of a prominent 3D deep conductive structure seen in the inversion of the southern array. To our surprise this deep southern feature is also imaged by the northern array even though it is well outside the footprint of the northern array. It therefore appears that typical intuition about one's ability to image structure outside the span of the sites is not always true. We present model studies to demonstrate why this is so and under what conditions one can expect a 3D array to be capable of imaging structure outside the array.

  4. Structural evolution of the Currawong Pb-Zn-Cu deposit (Victoria, Australia) - new insights from 3D implicit modelling linked to structural observations

    NASA Astrophysics Data System (ADS)

    Vollgger, Stefan; Cruden, Alexander

    2015-04-01

    Structurally controlled mineralisation commonly shows distinctive geometries, orientations and spatial distributions that derive from associated structures. These structures have the ability to effectively transport, trap and focus fluids. Moreover, structures such as faults and shear zones can offset, truncate and spatially redistribute earlier mineralisation. We present a workflow that combines structural fieldwork with state-of-the-art 3D modelling to assess the structural framework of an ore deposit. Traditional 3D models of ore deposits rely on manual digitisation of cross sections and their subsequent linkage to form 3D objects. Consequently, the geological interpretation associated with each section will be reflected in the resulting 3D models. Such models are therefore biased and should be viewed and interpreted with caution. Conversely, 3D implicit modelling minimises the modelling bias by using an implicit function that is fitted to spatial data such as drillhole data. This function defines a scalar field, from which 3D isosurfaces can be extracted. Assay data can be visualised as 3D grade shells at various threshold grade values and used to analyse and measure the shape, distribution and orientation of mineralisation. Additionally, lithology codes from drillholes can be used to extract lithological boundaries in 3D without the need for manual digitisation. In our case study at the Palaeozoic Currawong Pb-Zn-Cu deposit (Victoria, Australia), orientations extracted from ore bodies within a 3D implicit model have been compared to structural field data collected around the deposit. The data and model suggest that Currawong's massive sulfide lenses have been structurally modified. Mineralisation trends are parallel to a dominant NW dipping foliation mapped in the field. This foliation overprints earlier bedding in the host metasediments that has been deformed into upright folds. Several sets of steep faults further increase the structural complexity of the

  5. mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome.

    PubMed

    Meyer, Michael J; Lapcevic, Ryan; Romero, Alfonso E; Yoon, Mark; Das, Jishnu; Beltrán, Juan Felipe; Mort, Matthew; Stenson, Peter D; Cooper, David N; Paccanaro, Alberto; Yu, Haiyuan

    2016-05-01

    A new algorithm and Web server, mutation3D (http://mutation3d.org), proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web interface. On a large scale, we show that clustering with mutation3D is able to separate functional from nonfunctional mutations by analyzing a combination of 8,869 known inherited disease mutations and 2,004 SNPs overlaid together upon the same sets of crystal structures and homology models. Further, we present a systematic analysis of whole-genome and whole-exome cancer datasets to demonstrate that mutation3D identifies many known cancer genes as well as previously underexplored target genes. The mutation3D Web interface allows users to analyze their own mutation data in a variety of popular formats and provides seamless access to explore mutation clusters derived from over 975,000 somatic mutations reported by 6,811 cancer sequencing studies. The mutation3D Web interface is freely available with all major browsers supported. PMID:26841357

  6. Laser direct writing 3D structures for microfluidic channels: flow meter and mixer

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Lang; Liu, Yi-Jui; Lin, Zheng-Da; Wu, Bo-Long; Lee, Yi-Hsiung; Shin, Chow-Shing; Baldeck, Patrice L.

    2015-03-01

    The 3D laser direct-writing technology is aimed at the modeling of arbitrary three-dimensional (3D) complex microstructures by scanning a laser-focusing point along predetermined trajectories. Through the perspective technique, the details of designed 3D structures can be properly fabricated in a microchannel. This study introduces a direct reading flow meter and a 3D passive mixer fabricated by laser direct writing for microfluidic applications. The flow meter consists of two rod-shaped springs, a pillar, an anchor, and a wedge-shaped indicator, installed inside a microfluidic channel. The indicator is deflected by the flowing fluid while restrained by the spring to establish an equilibrium indication according to the flow rate. The measurement is readily carried out by optical microscopy observation. The 3D passive Archimedes-screw-shaped mixer is designed to disturb the laminar flow 3D direction for enhancing the mixing efficiency. The simulation results indicate that the screw provides 3D disturbance of streamlines in the microchannel. The mixing demonstration for fluids flowing in the micrchannel approximately agrees with the simulation result. Thanks to the advantage of the laser direct writing technology, this study performs the ingenious applications of 3D structures for microchannels.

  7. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  8. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  9. Numerical Models for Exploration and Visualization of Complex Geological Phenomena in an Undergraduate Structural Geology Course

    NASA Astrophysics Data System (ADS)

    Reinen, L. A.

    2008-12-01

    Computational science methods are often used to investigate and illustrate complex geological phenomena. To provide geology students with opportunities to both visualize and explore such phenomena, I have incorporated the program Poly3D into an undergraduate Structural Geology course. Poly3D is a three- dimensional boundary-element program developed at Stanford University, and is well suited to modeling joints and faults in a homogeneous, isotropic, linear-elastic whole or half space. In a series of guided inquiries throughout the course, students use Poly3D to explore the relationships between rock properties, joint/fault geometries, applied stresses or displacements, and the resultant deformation. With each subsequent assignment, student independence in the investigation increases, from initial visualizations of stresses at crack tips and investigation of controls on joint spacing, to individual and/or team proposals and research projects investigating specific student-generated questions in structural geology. I will present initial results from this teaching experiment and examples of the projects which have been executed, including the preparation students received to be able to use the program. Discussion and suggestions (particularly about effective means of conducting rigorous long-term assessment of student learning) are strongly encouraged.

  10. Use of x-ray microtomography for 3D imaging of internal structures

    NASA Astrophysics Data System (ADS)

    Hain, Miroslav; Bartl, Jan; Ševčík, Robert; Jacko, Vlado

    2012-01-01

    The article describes the basic principles and the use of X-ray microtomography which has emerged as a new promising method of measurement and non-destructive testing. X-ray microtomography (μCT) combines the principles of X-ray shadow microscopy together with the computed tomography CT. The current technical possibilities allow achieving submicron resolution by the use of experimental as well as commercial μCT facilities. Use of this method can be found particularly in materials research, precision engineering, and electronics industry. In all these areas there is a need for a non-destructive, high resolution visualization of internal microstructures, measurement of interior dimensions of 3D objects, materials testing for the presence of internal defects. Unlike the nondestructive μCT, the conventional testing methods require for the observation of internal structures mechanical cutting of the object and thus its destruction. Such damage of the object under study is often unacceptable, especially when it concerns an object of research, which should be preserved in integrity for its uniqueness or need to take further measurements and tests. Besides the materials research, there are also many other important areas of application of X-ray microtomography measuring method: electronics and precision mechanical engineering industry, mineralogy, geology, biology and archeology. In the experimental part of this article the results achieved in the microtomography laboratory of Slovak Academy of Sciences, equipped with the GE phoenix|x-ray nanotom 180 facility, will be presented.

  11. Effect of 3d doping on the electronic structure of BaFe2As2.

    PubMed

    McLeod, J A; Buling, A; Green, R J; Boyko, T D; Skorikov, N A; Kurmaev, E Z; Neumann, M; Finkelstein, L D; Ni, N; Thaler, A; Bud'ko, S L; Canfield, P C; Moewes, A

    2012-05-30

    The electronic structure of BaFe(2)As(2) doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d(10) shell. These findings help shed light on why superconductivity can occur in BaFe(2)As(2) doped with Co and Ni but not Cu. PMID:22534111

  12. Effect of 3d doping on the electronic structure of BaFe2As2

    SciTech Connect

    McLeod, John A.; Buling, A.; Green, R.J.; Boyko, T.D.; Skorikov, N.A.; Kurmaev, E.Z.; Neumann, M.; Finkelstein, L.D.; Ni, Ni; Thaler, Alexander; Budko, Serguei L.; Canfield, Paul; Moewes, A.

    2012-04-25

    The electronic structure of BaFe2As2 doped with Co, Ni and Cu has been studied by a variety of experimental and theoretical methods, but a clear picture of the dopant 3d states has not yet emerged. Herein we provide experimental evidence of the distribution of Co, Ni and Cu 3d states in the valence band. We conclude that the Co and Ni 3d states provide additional free carriers to the Fermi level, while the Cu 3d states are found at the bottom of the valence band in a localized 3d10 shell. These findings help shed light on why superconductivity can occur in BaFe2As2 doped with Co and Ni but not Cu.

  13. Evaluating integration of inland bathymetry in the U.S. Geological Survey 3D Elevation Program, 2014

    USGS Publications Warehouse

    Miller-Corbett, Cynthia

    2016-01-01

    Inland bathymetry survey collections, survey data types, features, sources, availability, and the effort required to integrate inland bathymetric data into the U.S. Geological Survey 3D Elevation Program are assessed to help determine the feasibility of integrating three-dimensional water feature elevation data into The National Map. Available data from wading, acoustic, light detection and ranging, and combined technique surveys are provided by the U.S. Geological Survey, National Oceanic and Atmospheric Administration, U.S. Army Corps of Engineers, and other sources. Inland bathymetric data accessed through Web-hosted resources or contacts provide useful baseline parameters for evaluating survey types and techniques used for collection and processing, and serve as a basis for comparing survey methods and the quality of results. Historically, boat-mounted acoustic surveys have provided most inland bathymetry data. Light detection and ranging techniques that are beneficial in areas hard to reach by boat, that can collect dense data in shallow water to provide comprehensive coverage, and that can be cost effective for surveying large areas with good water clarity are becoming more common; however, optimal conditions and techniques for collecting and processing light detection and ranging inland bathymetry surveys are not yet well defined.Assessment of site condition parameters important for understanding inland bathymetry survey issues and results, and an evaluation of existing inland bathymetry survey coverage are proposed as steps to develop criteria for implementing a useful and successful inland bathymetry survey plan in the 3D Elevation Program. These survey parameters would also serve as input for an inland bathymetry survey data baseline. Integration and interpolation techniques are important factors to consider in developing a robust plan; however, available survey data are usually in a triangulated irregular network format or other format compatible with

  14. 3-D Isotropic and Anisotropic S-velocity Structure in the North American Upper Mantle

    NASA Astrophysics Data System (ADS)

    Yuan, H.; Marone, F.; Romanowicz, B.; Abt, D.; Fischer, K.

    2008-12-01

    The tectonic diversity of the North American continent has led to a number of geological, tectonic and geodynamical models, many of which can be better tested with high resolution 3-d tomographic models of the isotropic and anisotropic mantle structure of the continent. In the framework of non-linear asymptotic coupling theory (NACT), we recently developed tools to invert long period seismic waveforms combined with SKS splitting data, for both isotropic and radial and azimuthal anisotropic S-wave velocity structure in the upper mantle at the continental scale (Marone et al., 2007; Marone and Romanowicz, 2007). Striking differences in both isotropic and anisotropic velocity structure were observed: beneath the high velocity stable cratonic region a distinct two-layer anisotropic domain is present, with the bottom layer fast axis direction aligned with the absolute plate motion, and a shallower lithospheric layer with north pointing fast axis most likely showing records of past tectonic history; under the active western US the direction of tomographically inferred anisotropy is stable with depth and compatible with the absolute plate motion direction. Here we present an updated model which includes nearly five more years of data, including data from newly operative USArray stations, and a somewhat more extended frequency band. Our new model confirms our previous results, and reveals greater yet complex details of the anisotropic velocity structure beneath the western U.S.. We also show initial results of incorporating constraints on the depth to the lithosphere-asthenosphere boundary (LAB) using teleseismic receiver functions. We discuss the different anisotropic domains resolved both laterally and in depth, in the context of tectonic history of the north American continent.

  15. Recovery and Visualization of 3D Structure of Chromosomes from Tomographic Reconstruction Images

    SciTech Connect

    Babu, S; Liao, P; Shin, M C; Tsap, L V

    2004-04-28

    The objectives of this work include automatic recovery and visualization of a 3D chromosome structure from a sequence of 2D tomographic reconstruction images taken through the nucleus of a cell. Structure is very important for biologists as it affects chromosome functions, behavior of the cell and its state. Chromosome analysis is significant in the detection of deceases and in monitoring environmental gene mutations. The algorithm incorporates thresholding based on a histogram analysis with a polyline splitting algorithm, contour extraction via active contours, and detection of the 3D chromosome structure by establishing corresponding regions throughout the slices. Visualization using point cloud meshing generates a 3D surface. The 3D triangular mesh of the chromosomes provides surface detail and allows a user to interactively analyze chromosomes using visualization software.

  16. 3D modeling of the Buhi debris avalanche deposit of Iriga Volcano, Philippines by integrating shallow-seismic reflection and geological data

    NASA Astrophysics Data System (ADS)

    Minimo, Likha G.; Lagmay, Alfredo Mahar Francisco A.

    2016-06-01

    Numerical models for simulating volcanic debris avalanches commonly lack a critical initiation parameter, the source volume, which is difficult to estimate without data on the deposit thickness. This, in turn, limits how rheology can be characterized for simulating flow. Leapfrog Geo, a 3D geological modeling software, was used to integrate shallow-seismic reflection profiles with field and borehole data to determine the volume of the Buhi debris avalanche and the pre-collapse structure of Iriga Volcano. Volumes of the deposit calculated in this way are 34-71% larger than previous estimates. This technique may improve models of debris avalanches elsewhere in the world, and more precisely depict landslide runout and lateral extent, thus improving disaster prevention and mitigation for the many cities located near volcanoes.

  17. 3-D Waveguide Effects of Topographical Structural Variation on Full Waveform Propagation: 3-D Finite Difference Modeling Comparisons with Field Data From Yuma Proving Ground, Arizona

    NASA Astrophysics Data System (ADS)

    Anderson, T. S.; Miller, R.; Greenfield, R.; Fisk, D.

    2002-12-01

    The propagation of seismic waves through regions of complex topography is not thoroughly understood. Surface waves, are of particular interest, as they are large in amplitude and can characterize the source depth, magnitude, and frequency content. The amplitude and frequency content of seismic waves that propagate in regions with large topographical variations are affected by both the scattering and blockage of the wave energy. The ability to predict the 3-d scattering due to topography will improve the understanding of both regional scale surface wave magnitudes, and refine surface wave discriminants as well as at the local scale (<2 km ) where it will aid in the development of rule of thumb guide lines for array sensor placement for real time sensing technologies. Ideally, when validating the numerical accuracy of a propagation model against field data, the input geologic parameters would be known and thus eliminates geology as a source of error in the calculation. In March of 2001, Kansas Geological Survey (KGS) performed a detailed seismic site characterization at the Smart Weapons Test Range, Yuma Proving Ground, Arizona. The result of the KGS characterization study is a high-resolution 3-d model that is used in our seismic simulations. The velocities Vs, Vp are calculated by tomography and refraction, attenuation coefficients estimated from the surface wave and from p-waves and are provided in a model with attributes resolved in 3-d to 0.5 meters. In the present work, we present comparisons of synthetic data with seismic data collected at the Smart Weapons Test Range to benchmark the accuracy achieved in simulating 3-d wave propagation in the vicinity of a topographical anomaly (trench). Synthetic seismograms are generated using a 3-d 8th order staggered grid visco-elastic finite difference code that accounts for topography. The geologic model is based on the Yuma site characterization. The size of these calculations required use of the DoD High Performance

  18. Improving Geologic and Engineering Models of Midcontinent Fracture and Karst-Modified Reservoirs Using New 3-D Seismic Attributes

    SciTech Connect

    Susan Nissen; Saibal Bhattacharya; W. Lynn Watney; John Doveton

    2009-03-31

    Our project goal was to develop innovative seismic-based workflows for the incremental recovery of oil from karst-modified reservoirs within the onshore continental United States. Specific project objectives were: (1) to calibrate new multi-trace seismic attributes (volumetric curvature, in particular) for improved imaging of karst-modified reservoirs, (2) to develop attribute-based, cost-effective workflows to better characterize karst-modified carbonate reservoirs and fracture systems, and (3) to improve accuracy and predictiveness of resulting geomodels and reservoir simulations. In order to develop our workflows and validate our techniques, we conducted integrated studies of five karst-modified reservoirs in west Texas, Colorado, and Kansas. Our studies show that 3-D seismic volumetric curvature attributes have the ability to re-veal previously unknown features or provide enhanced visibility of karst and fracture features compared with other seismic analysis methods. Using these attributes, we recognize collapse features, solution-enlarged fractures, and geomorphologies that appear to be related to mature, cockpit landscapes. In four of our reservoir studies, volumetric curvature attributes appear to delineate reservoir compartment boundaries that impact production. The presence of these compartment boundaries was corroborated by reservoir simulations in two of the study areas. Based on our study results, we conclude that volumetric curvature attributes are valuable tools for mapping compartment boundaries in fracture- and karst-modified reservoirs, and we propose a best practices workflow for incorporating these attributes into reservoir characterization. When properly calibrated with geological and production data, these attributes can be used to predict the locations and sizes of undrained reservoir compartments. Technology transfer of our project work has been accomplished through presentations at professional society meetings, peer-reviewed publications

  19. Modelling of Geological Structures Using Emergence

    NASA Astrophysics Data System (ADS)

    Hillier, M.; de Kemp, E. A.; Sprague, K.

    2009-05-01

    A complex system based approach is used to model geological structures. Preliminary work is presented to show how mutually interacting agents can be used to probe local regions and obtain emergent behaviour of its geometrical properties. Models are built bottom up from the smaller components to simulate regions from camp scales to regional scales. In nature, very complex structures exhibiting discontinuous and heterogeneous features are common. Modelling such regions using conventional methods is cumbersome and influences between close proximity zones are generally not considered. Agents are able to detect local and global features in the entire model space, as detailed as the data set allows. These features are incorporated into the interpolation of a modeled zone if those features are coupled to that location. We attempt to see if opportunities exist for exploiting complex systems approaches in what is a classical knowledge driven modelling domain with high emphasis on expert interpretive methods. Geological maps (2D, 3D or 4D) are fundamentally an emergent result of an iterative mental process which focuses on reconciling disparate data. The end goal of our research is to point a way forward in which complexity can support the simulation of maps and thus support the interpretive workflow.

  20. Transfer printing of 3D hierarchical gold structures using a sequentially imprinted polymer stamp.

    PubMed

    Zhang, Fengxiang; Low, Hong Yee

    2008-10-15

    Complex three-dimensional (3D) hierarchical structures on polymeric materials are fabricated through a process referred to as sequential imprinting. In this work, the sequentially imprinted polystyrene film is used as a soft stamp to replicate hierarchical structures onto gold (Au) films, and the Au structures are then transferred to a substrate by transfer printing at an elevated temperature and pressure. Continuous and isolated 3D structures can be selectively fabricated with the assistance of thermo-mechanical deformation of the polymer stamp. Hierarchical Au structures are achieved without the need for a corresponding three-dimensionally patterned mold. PMID:21832645

  1. Geometry of structures within crystalline bedrock constrained in 3D and their relevance for present day water infiltration.

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; de la Varga, Miguel; Florian Wellmann, J.; Kober, Florian; Berger, Alfons; Herwegh, Marco

    2016-04-01

    Fluid circulation in crystalline rocks is of key importance when exploring crystalline basement in light of, for example, deep-seated geothermal energy projects or selection of sites for nuclear waste repositories. Due to their enhanced permeability, fluid circulation within crystalline bedrock is mainly controlled by fault zones, which may originate from ductile mylonites but show a strong brittle overprint. In order to better constrain 3D flow paths, a well-founded knowledge on the 3D nature of the fault zone pattern is indispensable. We attempt to constrain the geometry of a complex 3D fault zone pattern in a case study of the Grimsel Test Site (GTS, central Switzerland). The constraints are based on mapping of both the surface as well as the GTS underground tunnel system, offering a unique opportunity to test the 3D model and associated uncertainties. We investigate the effect of increasing geoinformation on the quality and accuracy of the 3D model by using: (i) remote sensing surface data only, (ii) field surface mapping in combination with (i), and (iii) underground data combined with (i) and (ii). This approach allows for defining different steps in 3D geological modelling of a specific area, including a measure of the remaining uncertainty after each step. We obtain a best-estimate model by fitting results between surface and underground data by using a combination of field data and orientation obtained by Delaunay triangulation. We incorporate novel approaches to uncertainty analysis of fault orientations and investigate different fault planes showing the possible variation range of the structures investigated.

  2. Structure of Pseudoknot PK26 Shows 3D Domain Swapping in an RNA

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

    3D domain swapping provides a facile pathway for the evolution of oligomeric proteins and allosteric mechanisms and a means for using monomer-oligomer equilibria to regulate biological activity. The term "3D domain swapping" describes the exchange of identical domains between two protein monomers to create an oligomer. 3D domain swapping has, so far, only been recognized in proteins. In this study, the structure of the pseudoknot PK26 is reported and it is a clear example of 3D domain swapping in RNA. PK26 was chosen for study because RNA pseudoknots are required structures in several biological processes and they arise frequently in in vitro selection experiments directed against protein targets. PK26 specifically inhibits HIV-1 reverse transcriptase with nanomolar affinity. We have now determined the 3.1 A resolution crystal structure of PK26 and find that it forms a 3D domain swapped dimer. PK26 shows extensive base pairing between and within strands. Formation of the dimer requires the linker region between the pseudoknot folds to adopt a unique conformation that allows a base within a helical stem to skip one base in the stacking register. Rearrangement of the linker would permit a monomeric pseudoknot to form. This structure shows how RNA can use 3D domain swapping to build large scale oligomers like the putative hexamer in the packaging RNA of bacteriophage Phi29.

  3. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data

    PubMed Central

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUSstart) and after (3D-iCEUSend) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUSstart and 3D-iCEUSend data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  4. Vascular Structure Identification in Intraoperative 3D Contrast-Enhanced Ultrasound Data.

    PubMed

    Ilunga-Mbuyamba, Elisee; Avina-Cervantes, Juan Gabriel; Lindner, Dirk; Cruz-Aceves, Ivan; Arlt, Felix; Chalopin, Claire

    2016-01-01

    In this paper, a method of vascular structure identification in intraoperative 3D Contrast-Enhanced Ultrasound (CEUS) data is presented. Ultrasound imaging is commonly used in brain tumor surgery to investigate in real time the current status of cerebral structures. The use of an ultrasound contrast agent enables to highlight tumor tissue, but also surrounding blood vessels. However, these structures can be used as landmarks to estimate and correct the brain shift. This work proposes an alternative method for extracting small vascular segments close to the tumor as landmark. The patient image dataset involved in brain tumor operations includes preoperative contrast T1MR (cT1MR) data and 3D intraoperative contrast enhanced ultrasound data acquired before (3D-iCEUS s t a r t ) and after (3D-iCEUS e n d ) tumor resection. Based on rigid registration techniques, a preselected vascular segment in cT1MR is searched in 3D-iCEUS s t a r t and 3D-iCEUS e n d data. The method was validated by using three similarity measures (Normalized Gradient Field, Normalized Mutual Information and Normalized Cross Correlation). Tests were performed on data obtained from ten patients overcoming a brain tumor operation and it succeeded in nine cases. Despite the small size of the vascular structures, the artifacts in the ultrasound images and the brain tissue deformations, blood vessels were successfully identified. PMID:27070610

  5. Metal nanoparticle direct inkjet printing for low-temperature 3D micro metal structure fabrication

    NASA Astrophysics Data System (ADS)

    Ko, Seung Hwan; Chung, Jaewon; Hotz, Nico; Nam, Koo Hyun; Grigoropoulos, Costas P.

    2010-12-01

    Inkjet printing of functional materials is a key technology toward ultra-low-cost, large-area electronics. We demonstrate low-temperature 3D micro metal structure fabrication by direct inkjet printing of metal nanoparticles (NPs) as a versatile, direct 3D metal structuring approach representing an alternative to conventional vacuum deposition and photolithographic methods. Metal NP ink was inkjet-printed to exploit the large melting temperature drop of the nanomaterial and the ease of the NP ink formulation. Parametric studies on the basic conditions for stable 3D inkjet printing of NP ink were carried out. Furthermore, diverse 3D metal microstructures, including micro metal pillar arrays, helices, zigzag and micro bridges were demonstrated and electrical characterization was performed. Since the process requires low temperature, it carries substantial potential for fabrication of electronics on a plastic substrate.

  6. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  7. Air-structured optical fibre drawn from a 3D-printed preform

    NASA Astrophysics Data System (ADS)

    Cook, Kevin; Leon-Saval, Sergio; Canning, John; Reid, Zane; Hossain, Md. Arafat; Peng, Gang-Ding

    2015-09-01

    We report the first optical fibre drawn from a 3D-printed preform. An air-structured polymer preform is printed using a modified butadiene plastic called Bendlay as opposed to the more-common Acrylonitrile Butadiene Styrene (ABS). The preform is subsequently drawn to fibre form at a relatively low temperature of 160 °C and maintains its air-structured cladding holes. Such ability to freely-design and 3D-print complex preform structures, such as photonic bandgap and photonic crystal structures, opens up an exciting new front in optical fibre fabrication.

  8. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes

    PubMed Central

    Rodriguez-Palacios, Alex; Kodani, Tomohiro; Kaydo, Lindsey; Pietropaoli, Davide; Corridoni, Daniele; Howell, Scott; Katz, Jeffry; Xin, Wei; Pizarro, Theresa T.; Cominelli, Fabio

    2015-01-01

    Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes (‘cobblestones' versus ‘villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals ‘liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD. PMID:26154811

  9. A finite element analysis of a 3D auxetic textile structure for composite reinforcement

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

    This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites.

  10. Gene3D: structural assignments for the biologist and bioinformaticist alike

    PubMed Central

    Buchan, Daniel W. A.; Rison, Stuart C. G.; Bray, James E.; Lee, David; Pearl, Frances; Thornton, Janet M.; Orengo, Christine A.

    2003-01-01

    The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH. PMID:12520054

  11. Simultaneous inversion for 3D crustal and anisotropic lithospheric structure and regional hypocenters beneath Germany

    NASA Astrophysics Data System (ADS)

    Muench, Thomas; Koch, Manfred; Schlittenhardt, Jörg

    2010-05-01

    There is now ample evidence from both refraction seismic studies, done already a quarter century ago and from more recent local earthquake traveltime analysis of some of the authors above that large sections of the upper mantle underneath Europe and Germany, in particular, are anisotropic. Employing a modified version of the method of simultaneous inversion for structure and hypocenters (SSH) of the first author, including a priori known upper mantle anisotropy, the investigations of Song et al. [2001] and Song et al. [2004] by means of a 1D time-term analysis and a full 2D Pn anisotropic inversion of regional traveltime data are extended here to a full 3D SSH-inversion underneath Germany. Regional traveltimes from local events occurring between 1975 - 2003 are used which, after application of several selection criteria, results in ~1300 events with a total of ~30000 P- and S-phases for the SSH inversion. Because many of the recorded events appear to suffer from relatively poor hypocentral depth locations a full SSH analysis becomes an intricate undertaking. To alleviate the problem the SSH procedure is carried out in several incremental steps of increasing complexity. First of all improved vertically inhomogeneous velocity (1D) models are derived assuming an isotropic as well as an anisotropic upper mantle. In addition of a slightly better model fit for the anisotropic than for the isotropic model, the latter gives also a somewhat lower Pn-velocity of ~7.90 km/s, compared with ~8.0 km/s for the former. This indicates that inclusion of upper mantle anisotropy into the model is required to obtain physically reasonable Pn-velocities. The results for the P-velocity in the lower crustal layer of the model are less clear, as there appears to be some trade-off in the velocity of that layer and that of the upper mantle. During the course of this part of the study the 3D models have been increasingly refined, starting with a lateral discretization into 15 x 15 blocs

  12. Determining the 3D Subsurface Density Structure of Taurus Littrow Valley Using Apollo 17 Gravity Data

    NASA Technical Reports Server (NTRS)

    Urbancic, N.; Ghent, R.; Stanley, S,; Johnson, C. L.; Carroll, K. A.; Hatch, D.; Williamson, M. C.; Garry, W. B.; Talwani, M.

    2016-01-01

    Surface gravity surveys can detect subsurface density variations that can reveal subsurface geologic features. In 1972, the Apollo 17 (A17) mission conducted the Traverse Gravimeter Experiment (TGE) using a gravimeter that measured the local gravity field near Taurus Littrow Valley (TLV), located on the south-eastern rim of the Serenitatis basin. TLV is hypothesized to be a basaltfilled radial graben resulting from the impact that formed Mare Serenitatis. It is bounded by both the North and South Massifs (NM and SM) as well as other smaller mountains to the East that are thought to be mainly composed of brecciated highland material. The TGE is the first and only successful gravity survey on the surface of the Moon. Other more recent satellite surveys, such as NASA's Gravity Recovery and Interior Laboratory (GRAIL) mission (2011- 2012), have produced the best global gravity field to date (approx. 13km resolution). However, these satellite surveys are not sensitive enough to detect fine-scale (<1km) lunar subsurface structures. This underscores the value of the data collected at the surface by A17. In the original analysis of the data a 2D forward-modelling approach was used to derive a thickness of the subsurface basalt layer of 1.0 km by assuming a simple flat-faced rectangular geometry and using densities derived from Apollo lunar samples. We are investigating whether modern 3D modelling techniques in combination with high-resolution topographical and image datasets can reveal additional fine-scale subsurface structure in TLV.

  13. Geological and petrophysical characterization of the Ferron Sandstone for 3-D simulation of a fluvial-deltaic reservoir. [Quarterly] report, January 1--March 31, 1994

    SciTech Connect

    Allison, M.L.

    1994-04-22

    The objective of this project is to develop a comprehensive, interdisciplinary, quantitative characterization of a fluvial-deltaic reservoir which will allow realistic interwell and reservoir-scale modeling to be used for improved oil-field development in similar reservoirs world wide. The geological and petrophysical properties of the Cretaceous Ferron Sandstone in east-central Utah will be quantitatively determined. Both new and existing data will be integrated into a 3-D representation of spatial variations in porosity, storativity, and tensorial rock permeability at a scale appropriate for interwell to regional-scale reservoir simulation. Results could improve reservoir management through proper infill and extension drilling strategies, reduce economic risks, increase recovery from existing oil fields, and provide more reliable reserve calculations. Transfer of the project results to the petroleum industry will be an integral component of the project. The technical progress is divided into several sections corresponding to subtasks outlined in the Regional Stratigraphy Task and the Case Studies Task of the original proposal. The primary objective of the Regional Stratigraphy Task is to provide a more detailed interpretation of the stratigraphy of the Ferron Sandstone outcrop belt from Last Chance Creek to Ferron Creek. The morphological framework established from the case studies will be used to generate subsequent flow models for the reservoir types. The primary objective of the Case Study Task is to develop a detailed geological and petrophysical characterization, at well-sweep scale or smaller, of the primary reservoir lithofacies typically found in a fluvial-dominated deltaic reservoir. Sedimentary structures, lithofacies, bounding surfaces, and permeabilities measured along closely spaced traverses (both vertical and horizontal) will be combined with data from core drilling to develop a 3-D morphology of the reservoirs within each case study area.

  14. Towards "realistic" fault zones in a 3D structure model of the Thuringian Basin, Germany

    NASA Astrophysics Data System (ADS)

    Kley, J.; Malz, A.; Donndorf, S.; Fischer, T.; Zehner, B.

    2012-04-01

    3D computer models of geological architecture are evolving into a standard tool for visualization and analysis. Such models typically comprise the bounding surfaces of stratigraphic layers and faults. Faults affect the continuity of aquifers and can themselves act as fluid conduits or barriers. This is one reason why a "realistic" representation of faults in 3D models is desirable. Still so, many existing models treat faults in a simplistic fashion, e.g. as vertical downward projections of fault traces observed at the surface. Besides being geologically and mechanically unreasonable, this also causes technical difficulties in the modelling workflow. Most natural faults are inclined and may change dips according to rock type or flatten into mechanically weak layers. Boreholes located close to a fault can therefore cross it at depth, resulting in stratigraphic control points allocated to the wrong block. Also, faults tend to split up into several branches, forming fault zones. Obtaining a more accurate representation of faults and fault zones is therefore challenging. We present work-in-progress from the Thuringian Basin in central Germany. The fault zone geometries are never fully constrained by data and must be extrapolated to depth. We use balancing of serial, parallel cross-sections to constrain subsurface extrapolations. The structure sections are checked for consistency by restoring them to an undeformed state. If this is possible without producing gaps or overlaps, the interpretation is considered valid (but not unique) for a single cross-section. Additional constraints are provided by comparison of adjacent cross-sections. Structures should change continuously from one section to another. Also, from the deformed and restored cross-sections we can measure the strain incurred during deformation. Strain should be compatible among the cross-sections: If at all, it should vary smoothly and systematically along a given fault zone. The stratigraphic contacts and

  15. Lithographically-generated 3D lamella layers and their structural color

    NASA Astrophysics Data System (ADS)

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-01

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ~ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc.

  16. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  17. Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

    The CATH database is a classification of protein structures found in the Protein Data Bank (PDB). Protein structures are chopped into individual units of structural domains, and these domains are grouped together into superfamilies if there is sufficient evidence that they have diverged from a common ancestor during the process of evolution. A sister resource, Gene3D, extends this information by scanning sequence profiles of these CATH domain superfamilies against many millions of known proteins to identify related sequences. Thus the combined CATH-Gene3D resource provides confident predictions of the likely structural fold, domain organisation, and evolutionary relatives of these proteins. In addition, this resource incorporates annotations from a large number of external databases such as known enzyme active sites, GO molecular functions, physical interactions, and mutations. This unit details how to access and understand the information contained within the CATH-Gene3D Web pages, the downloadable data files, and the remotely accessible Web services. PMID:26087950

  18. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

    Nugraha, Andri Dian; Syahputra, Ahmad; Fatkhan,; Sule, Rachmat

    2013-09-09

    We conducted delay time tomography to determine 3-D seismic velocity structures (Vp, Vs, and Vp/Vs ratio) using micro-seismic events in the geothermal field. The P-and S-wave arrival times of these micro-seismic events have been used as input for the tomographic inversion. Our preliminary seismic velocity results show that the subsurface condition of geothermal field can be fairly delineated the characteristic of reservoir. We then extended our understanding of the subsurface physical properties through determining of attenuation structures (Qp, Qs, and Qs/Qp ratio) using micro-seismic waveform. We combined seismic velocities and attenuation structures to get much better interpretation of the reservoir characteristic. Our preliminary attanuation structures results show reservoir characterization can be more clearly by using the 3-D attenuation model of Qp, Qs, and Qs/Qp ratio combined with 3-D seismic velocity model of Vp, Vs, and Vp/Vs ratio.

  19. Lithographically-generated 3D lamella layers and their structural color.

    PubMed

    Zhang, Sichao; Chen, Yifang; Lu, Bingrui; Liu, Jianpeng; Shao, Jinhai; Xu, Chen

    2016-04-28

    Inspired by the structural color from the multilayer nanophotonic structures in Morpho butterfly wing scales, 3D lamellae layers in dielectric polymers (polymethyl methacrylate, PMMA) with n ∼ 1.5 were designed and fabricated by standard top-down electron beam lithography with one-step exposure followed by an alternating development/dissolution process of PMMA/LOR (lift-off resist) multilayers. This work offers direct proof of the structural blue/green color via lithographically-replicated PMMA/air multilayers, analogous to those in real Morpho butterfly wings. The success of nanolithography in this work for the 3D lamellae structures in dielectric polymers not only enables us to gain deeper insight into the mysterious blue color of the Morpho butterfly wings, but also breaks through the bottleneck in technical development toward broad applications in gas/liquid sensors, 3D meta-materials, coloring media, and infrared imaging devices, etc. PMID:27087577

  20. System for conveyor belt part picking using structured light and 3D pose estimation

    NASA Astrophysics Data System (ADS)

    Thielemann, J.; Skotheim, Ø.; Nygaard, J. O.; Vollset, T.

    2009-01-01

    Automatic picking of parts is an important challenge to solve within factory automation, because it can remove tedious manual work and save labor costs. One such application involves parts that arrive with random position and orientation on a conveyor belt. The parts should be picked off the conveyor belt and placed systematically into bins. We describe a system that consists of a structured light instrument for capturing 3D data and robust methods for aligning an input 3D template with a 3D image of the scene. The method uses general and robust pre-processing steps based on geometric primitives that allow the well-known Iterative Closest Point algorithm to converge quickly and robustly to the correct solution. The method has been demonstrated for localization of car parts with random position and orientation. We believe that the method is applicable for a wide range of industrial automation problems where precise localization of 3D objects in a scene is needed.

  1. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

    3D printing is a form of additive manufacturing whereby the building up of layers of material creates objects. The selective laser sintering process (SLS) uses a laser beam to sinter powdered material to create objects. This paper builds upon previous research into 3D printed textile based material exploring the use of SLS using nylon powder to create flexible weft knitted structures. The results show the potential to print flexible textile based structures that exhibit the properties of traditional knitted textile structures along with the mechanical properties of the material used, whilst describing the challenges regarding fineness of printing resolution. The conclusion highlights the potential future development and application of such pieces.

  2. Acquisition of 3d Information for Vanished Structure by Using Only AN Ancient Picture

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

    In order to acquire 3D information for reconstruction of vanished historical structure, grasp of 3D shape of such structure was attempted by using an ancient picture. Generally, 3D information of a structure is acquired by photogrammetric theory which requires two or more pictures. This paper clarifies that the geometrical information of the structure was obtained only from an ancient picture, and 3D information was acquired. This kind of method was applied for an ancient picture of the Old Imperial Theatre. The Old Imperial Theatre in the picture is constituted by two-point perspective. Therefore, estimated value of focal length of camera, length of camera to the Old Imperial Theatre and some parameters were calculated by estimation of field angle, using body height as an index of length and some geometrical information. Consequently, 3D coordinate of 120 measurement points on the surface of the Old Imperial Theatre were calculated respectively, and 3DCG modeling of the Old Imperial Theatre was realized.

  3. Characterisation of the surface structure of 3D printed scaffolds for cell infiltration and surgical suturing.

    PubMed

    Ruiz-Cantu, Laura; Gleadall, Andrew; Faris, Callum; Segal, Joel; Shakesheff, Kevin; Yang, Jing

    2016-03-01

    3D printing is of great interest for tissue engineering scaffolds due to the ability to form complex geometries and control internal structures, including porosity and pore size. The porous structure of scaffolds plays an important role in cell ingrowth and nutrition infusion. Although the internal porosity and pore size of 3D printed scaffolds have been frequently studied, the surface porosity and pore size, which are critical for cell infiltration and mass transport, have not been investigated. The surface geometry can differ considerably from the internal scaffold structure depending on the 3D printing process. It is vital to be able to control the surface geometry of scaffolds as well as the internal structure to fabricate optimal architectures. This work presents a method to control the surface porosity and pore size of 3D printed scaffolds. Six scaffold designs have been printed with surface porosities ranging from 3% to 21%. We have characterised the overall scaffold porosity and surface porosity using optical microscopy and microCT. It has been found that surface porosity has a significant impact on cell infiltration and proliferation. In addition, the porosity of the surface has been found to have an effect on mechanical properties and on the forces required to penetrate the scaffold with a surgical suturing needle. To the authors' knowledge, this study is the first to investigate the surface geometry of extrusion-based 3D printed scaffolds and demonstrates the importance of surface geometry in cell infiltration and clinical manipulation. PMID:26930179

  4. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

    Zawadzki, Robert J.; Fuller, Alfred R.; Zhao, Mingtao; Wiley, David F.; Choi, Stacey S.; Bower, Bradley A.; Hamann, Bernd; Izatt, Joseph A.; Werner, John S.

    2006-02-01

    The acquisition speed of current FD-OCT (Fourier Domain - Optical Coherence Tomography) instruments allows rapid screening of three-dimensional (3D) volumes of human retinas in clinical settings. To take advantage of this ability requires software used by physicians to be capable of displaying and accessing volumetric data as well as supporting post processing in order to access important quantitative information such as thickness maps and segmented volumes. We describe our clinical FD-OCT system used to acquire 3D data from the human retina over the macula and optic nerve head. B-scans are registered to remove motion artifacts and post-processed with customized 3D visualization and analysis software. Our analysis software includes standard 3D visualization techniques along with a machine learning support vector machine (SVM) algorithm that allows a user to semi-automatically segment different retinal structures and layers. Our program makes possible measurements of the retinal layer thickness as well as volumes of structures of interest, despite the presence of noise and structural deformations associated with retinal pathology. Our software has been tested successfully in clinical settings for its efficacy in assessing 3D retinal structures in healthy as well as diseased cases. Our tool facilitates diagnosis and treatment monitoring of retinal diseases.

  5. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  6. Structural response to 3D simulated earthquake motions in San Bernardino Valley

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

    Structural repsonse to one- and three-dimensional (3D) simulated motions in San Bernardino Valley from a hypothetical earthquake along the San Andreas fault with moment magnitude 6.5 and rupture length of 30km is investigated. The results show that the ground motions and the structural response vary dramatically with the type of simulation and the location. -from Authors

  7. The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture.

    PubMed

    Markaki, Yolanda; Smeets, Daniel; Fiedler, Susanne; Schmid, Volker J; Schermelleh, Lothar; Cremer, Thomas; Cremer, Marion

    2012-05-01

    Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization. PMID:22508100

  8. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  9. The upper crustal 3-D resistivity structure of the Kristineberg area, Skellefte district, northern Sweden revealed by magnetotelluric data

    NASA Astrophysics Data System (ADS)

    Hübert, Juliane; Juanatey, María de los Ángeles García; Malehmir, Alireza; Tryggvason, Ari; Pedersen, Laust B.

    2013-02-01

    A 3-D model of the crustal electrical resistivity was constructed from the inversion of magnetotelluric data in the Kristineberg area, Skellefte district, the location of one of Sweden's most successful mining activities. Forward modelling of vertical magnetic transfer data supports our model which was derived from the magnetotelluric impedance only. The dominant features in the 3-D model are the strong conductors at various depth levels and resistive bodies of variable thickness occurring in the shallower subsurface. The deepest conductor, previously associated with the Skellefte crustal conductivity anomaly, is imaged in the southern part of the area as a north-dipping feature starting at ˜4 km depth. Several shallow conductors are attributed to graphite in the black shales defining the contact between the metasedimentary rocks and the underlying metavolcanic rocks. Furthermore, an elongated intermediate depth conductor is possibly associated with alteration zones in the metavolcanic rocks that host the ore occurrences. The most prominent crustal resistors occur in the southern and northern part of the area, where their lateral extent on the surface coincides with the late-orogenic Revsund type intrusions. To the east, a resistive feature can be correlated to the early-orogenic Viterliden intrusion. The 3-D model is compared with two previous 2-D inversion models along two perpendicular profiles. The main electrical features are confirmed with the new model and previous uncertainties regarding 3-D effects, caused by off-profile conductors, can be better assessed in 3-D, although the resolution is lower due to a coarser model discretization. The comparison with seismic sections along two north-south profiles reveals structural correspondence between electrical features, zones of different reflectivity and geological units.

  10. Advanced methods for 3-D inelastic structural analysis for hot engine structures

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

    Three-dimensional Inelastic Analysis Methods are described. These methods were incorporated into a series of new computer codes embodying a progression of mathematical models (mechanics of materials, specialty finite element, boundary element) for streamlined analysis of hot engine structures such as: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain) and global (displacements, frequencies, amplitudes, buckling) structural behavior of the three respective components. The methods and the three computer codes, referred to as MOMM (Mechanics Of Materials Model), MHOST (MARC-Hot Section Technology), and BEST3D (Boundary Element Stress Technology), have been developed and are briefly described.

  11. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

    Madura, Thomas; Gull, Theodore R.; Clementel, Nicola; Paardekooper, Jan-Pieter; Kruip, Chael; Corcoran, Michael F.; Hamaguchi, Kenji; Teodoro, Mairan

    2015-01-01

    We present the first 3D prints of output from a supercomputer simulation of a complex astrophysical system, the colliding stellar winds in the massive (>120 MSun), highly eccentric (e ~ 0.9) binary Eta Carinae. Using a consumer-grade 3D printer (Makerbot Replicator 2X), we successfully printed 3D smoothed particle hydrodynamics simulations of Eta Carinae's inner (r ~110 AU) wind-wind collision interface at multiple orbital phases. These 3D prints reveal important, previously unknown 'finger-like' structures at orbital phases shortly after periastron (φ ~1.045) that protrude radially outward from the spiral wind-wind collision region. We speculate that these fingers are related to instabilities (e.g. Rayleigh-Taylor) that arise at the interface between the radiatively-cooled layer of dense post-shock primary-star wind and the hot, adiabatic post-shock companion-star wind. The success of our work and easy identification of previously unknown physical features highlight the important role 3D printing can play in the visualization and understanding of complex 3D time-dependent numerical simulations of astrophysical phenomena.

  12. 3D P-Wave Velocity Structure of the Deep Galicia Rifted Margin

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy; Davy, Richard; Sawyer, Dale; Klaeschen, Dirk; Papenberg, Cord; Reston, Timothy; Shillington, Donna; Ranero, Cesar

    2015-04-01

    The combined wide-angle reflection-refraction and multi-channel seismic (MCS) experiment, Galicia 3D, was carried out in 2013 at the Galicia rifted margin in the northeast Atlantic Ocean, west of Spain. The main geological features within the 64 by 20 km (1280 km²) 3D box investigated by the survey are the peridotite ridge (PR), the fault bounded, rotated basement blocks and the S reflector, which has been interpreted to be a low angle detachment fault. 44 short period four-component ocean bottom seismometers and 28 ocean bottom hydrophones were deployed in the 3D box. 3D MCS profiles sampling the whole box were acquired with two airgun arrays of 3300 cu.in. fired alternately every 37.5 m. We present the results from 3D first-arrival time tomography that constrains the P-wave velocity in the 3D box, for the entire depth sampled by reflection data. Results are validated by synthetic tests and by the comparison with Galicia 3D MCS lines. The main outcomes are as follows: 1- The 3.5 km/s iso-velocity contour mimics the top of the acoustic basement observed on MCS profiles. Block bounding faults are imaged as velocity contrasts and basement blocks exhibit 3D topographic variations. 2- On the southern profiles, the top of the PR rises up to 5.5 km depth whereas, 20 km northward, its basement expression (at 6.5 km depth) nearly disappears. 3- The 6.5 km/s iso-velocity contour matches the topography of the S reflector where the latter is visible on MCS profiles. Within a depth interval of 0.6 km (in average), velocities beneath the S reflector increase from 6.5 km/s to 7 km/s, which would correspond to a decrease in the degree of serpentinization from ~45 % to ~30 % if these velocity variations are caused solely by variations in hydration. At the intersections between the block bounding normal faults and the S reflector, this decrease happens over a larger depth interval (> 1 km), suggesting that faults act as conduit for the water flow in the upper mantle.

  13. Direct-growth carbon nanotubes on 3D structural microelectrodes for electrophysiological recording.

    PubMed

    Pan, Alice Ian; Lin, Min-Hsuan; Chung, Hui-Wen; Chen, Hsin; Yeh, Shih-Rung; Chuang, Yung-Jen; Chang, Yen-Chung; Yew, Tri-Rung

    2016-01-01

    A novel 3D carbon nanotube (CNT) microelectrode was developed through direct growth of CNTs on a gold pin-shaped 3D microelectrode at a low temperature (400 °C) for applications in neural and cardiac recording. With an electroplated Ni catalyst layer covering the entire surface of the pin-shaped structure, CNTs were synthesized on a 3D microelectrode by catalytic thermal chemical vapor deposition (CVD). According to the analyses by electrochemical impedance spectroscopy, the impedance of 3D microelectrodes after CNT growth and UV/O3 treatment decreased from 9.3 Ω mm(-2) to 1.2 Ω mm(-2) and the capacitance increased largely from 2.2 mF cm(-2) to 73.3 mF cm(-2). The existence of UVO3-treated CNT led to a large improvement of interfacial capacitance, contributing to the decrease of impedance. The electrophysiological detection capability of this 3D CNT microelectrode was demonstrated by the distinguished P waves, QRS complex and T waves in the electrocardiogram of the zebrafish heart and the action potential recorded from individual rat hippocampal neurons. The compatibility of integration with ICs, high resolution in space, electrophysiological signals, and non-invasive long-term recording suggest that the 3D CNT microelectrode exhibits promising potential for applications in electrophysiological research and clinical trials. PMID:26588673

  14. 2D and 3D X-Ray Structural Microscopy Using Submicron-Resolution Laue Microdiffraction

    SciTech Connect

    Budai, John D.; Yang, Wenge; Larson, Bennett C.; Tischler, Jonathan Z.; Liu, Wenjun; Ice, Gene E.

    2010-11-10

    We have developed a scanning, polychromatic x-ray microscopy technique with submicron spatial resolution at the Advanced Photon Source. In this technique, white undulator radiation is focused to submicron diameter using elliptical mirrors. Laue diffraction patterns scattered from the sample are collected with an area detector and then analyzed to obtain the local crystal structure, lattice orientation, and strain tensor. These new microdiffraction capabilities have enabled both 2D and 3D structural studies of materials on mesoscopic length-scales of tenths-to-hundreds of microns. For thin samples such as deposited films, 2D structural maps are obtained by step-scanning the area of interest. For example, 2D x-ray microscopy has been applied in studies of the epitaxial growth of oxide films. For bulk samples, a 3D differential-aperture x-ray microscopy technique has been developed that yields the full diffraction information from each submicron volume element. The capabilities of 3D x-ray microscopy are demonstrated here with measurements of grain orientations and grain boundary motion in polycrystalline aluminum during 3D thermal grain growth. X-ray microscopy provides the needed, direct link between the experimentally measured 3D microstructural evolution and the results of theory and modeling of materials processes on mesoscopic length scales.

  15. Local-global alignment for finding 3D similarities in protein structures

    DOEpatents

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  16. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  17. Multi-scale modelling of strongly heterogeneous 3D composite structures using spatial Voronoi tessellation

    NASA Astrophysics Data System (ADS)

    El Said, Bassam; Ivanov, Dmitry; Long, Andrew C.; Hallett, Stephen R.

    2016-03-01

    3D composite materials are characterized by complex internal yarn architectures, leading to complex deformation and failure development mechanisms. Net-shaped preforms, which are originally periodic in nature, lose their periodicity when the fabric is draped, deformed on a tool, and consolidated to create geometrically complex composite components. As a result, the internal yarn architecture, which dominates the mechanical behaviour, becomes dependent on the structural geometry. Hence, predicting the mechanical behaviour of 3D composites requires an accurate representation of the yarn architecture within structural scale models. When applied to 3D composites, conventional finite element modelling techniques are limited to either homogenised properties at the structural scale, or the unit cell scale for a more detailed material property definition. Consequently, these models fail to capture the complex phenomena occurring across multiple length scales and their effects on a 3D composite's mechanical response. Here a multi-scale modelling approach based on a 3D spatial Voronoi tessellation is proposed. The model creates an intermediate length scale suitable for homogenisation to deal with the non-periodic nature of the final material. Information is passed between the different length scales to allow for the effect of the structural geometry to be taken into account on the smaller scales. The stiffness and surface strain predictions from the proposed model have been found to be in good agreement with experimental results. The proposed modelling framework has been used to gain important insight into the behaviour of this category of materials. It has been observed that the strain and stress distributions are strongly dependent on the internal yarn architecture and consequently on the final component geometry. Even for simple coupon tests, the internal architecture and geometric effects dominate the mechanical response. Consequently, the behaviour of 3D woven

  18. Computational methods for constructing protein structure models from 3D electron microscopy maps

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

    Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3 Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. PMID:23796504

  19. Segmented images and 3D images for studying the anatomical structures in MRIs

    NASA Astrophysics Data System (ADS)

    Lee, Yong Sook; Chung, Min Suk; Cho, Jae Hyun

    2004-05-01

    For identifying the pathological findings in MRIs, the anatomical structures in MRIs should be identified in advance. For studying the anatomical structures in MRIs, an education al tool that includes the horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is necessary. Such an educational tool, however, is hard to obtain. Therefore, in this research, such an educational tool which helps medical students and doctors study the anatomical structures in MRIs was made as follows. A healthy, young Korean male adult with standard body shape was selected. Six hundred thirteen horizontal MRIs of the entire body were scanned and inputted to the personal computer. Sixty anatomical structures in the horizontal MRIs were segmented to make horizontal segmented images. Coronal, sagittal MRIs and coronal, sagittal segmented images were made. 3D images of anatomical structures in the segmented images were reconstructed by surface rendering method. Browsing software of the MRIs, segmented images, and 3D images was composed. This educational tool that includes horizontal, coronal, sagittal MRIs of entire body, corresponding segmented images, 3D images, and browsing software is expected to help medical students and doctors study anatomical structures in MRIs.

  20. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

    Heller, L.; Vokoun, D.; Šittner, P.; Finckh, H.

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

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

    PubMed

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

    2016-07-01

    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. PMID:27095203

  2. The 3D crustal structure of Northeastern Tibetan area from seismic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Anhui

    2015-04-01

    The Northeastern Tibetan region is located in the border area of three sub-plates in China, i.e. the Tibetan plateau, North China block and Xinjiang block. Effected simultaneously by the extrusion driven by the India-Eurasia plat collision and the blockage of the Ordos basin, this area has complex geology, strong tectonics activities and suffered from several large historic earthquakes, such as the Haiyuan earthquake (M8.6) in 1920, the Gulang earthquake (M8.0) in 1927. To enhance our understanding of the crustal structure and the interaction between different tectonic blocks of this region, we conduct a three-dimensional (3D) tomographic study by using the arrival time date recorded by regional seismic network. We used 101101 P and 103313 S wave arrival times from 11650 local earthquakes during 1970 to 2013 recorded by 154 permanent seismic stations of the local Seismic Network, installed over five provinces in China, i.e. Gansu, Ningxia, Qinghai, Shanxi, Neimenggu. We first established a 1D primary crustal model from LITHO1.0, an updated crust and lithospheric model of the Earth by weighted averaging. To better performer ray tracing, our inversion involved three discontinuities (including the Moho) with depth variation over the mantle derived from LITHO1.0. Detailed three-dimensional seismic velocity (Vp and Vs) structures of the crust of the Northeastern Tibetan are determined with a horizontal resolution of about 35 km and a depth resolution of 6-20 km. The Poisson's ratio (σ) structure was also estimated after obtained Vp and Vs structures. We detected low-velocity anomalies in the lower crust and relative high-velocity anomalies in the upper crust beneath the Longmenshan faults zone, which are in good agreement with the results of most previous geophysical studies. Our results revealed clear different velocity variation beneath both sides of different tectonic blocks. In addition, we found the correlation between our tomographic result and previous

  3. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

  4. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  5. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  6. Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media

    NASA Astrophysics Data System (ADS)

    Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben

    2014-09-01

    We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.

  7. Element-specific X-ray phase tomography of 3D structures at the nanoscale.

    PubMed

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Holler, Mirko; Huthwelker, Thomas; Menzel, Andreas; Vartiainen, Ismo; Müller, Elisabeth; Kirk, Eugenie; Gliga, Sebastian; Raabe, Jörg; Heyderman, Laura J

    2015-03-20

    Recent advances in fabrication techniques to create mesoscopic 3D structures have led to significant developments in a variety of fields including biology, photonics, and magnetism. Further progress in these areas benefits from their full quantitative and structural characterization. We present resonant ptychographic tomography, combining quantitative hard x-ray phase imaging and resonant elastic scattering to achieve ab initio element-specific 3D characterization of a cobalt-coated artificial buckyball polymer scaffold at the nanoscale. By performing ptychographic x-ray tomography at and far from the Co K edge, we are able to locate and quantify the Co layer in our sample to a 3D spatial resolution of 25 nm. With a quantitative determination of the electron density we can determine that the Co layer is oxidized, which is confirmed with microfluorescence experiments. PMID:25839287

  8. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  9. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  10. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

  11. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  12. RNAssess--a web server for quality assessment of RNA 3D structures.

    PubMed

    Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz; Szachniuk, Marta; Popenda, Mariusz; Adamiak, Ryszard W; Blazewicz, Jacek

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. PMID:26068469

  13. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  14. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  15. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  16. Structural analysis of San Leo (RN, Italy) east and north cliffs using 3D point clouds

    NASA Astrophysics Data System (ADS)

    Spreafico, Margherita Cecilia; Bacenetti, Marco; Borgatti, Lisa; Cignetti, Martina; Giardino, Marco; Perotti, Luigi

    2013-04-01

    The town of San Leo, like many others in the historical region of Montefeltro (Northern Apennines, Italy), was built in medieval period on a calcarenite and sandstone slab, bordered by subvertical and overhanging cliffs up to 100 m high, for defense purposes. The slab and the underlying clayey substratum show widespread landslide phenomena: the first is tectonized and crossed by joints and faults, and it is affected by lateral spreading with associated rock falls, topples and tilting. Moreover, the underlying clayey substratum is involved in plastic movements, like earth flows and slides. The main cause of instability in the area, which brings about these movements, is the high deformability contrast between the plate and the underlying clays. The aim of our research is to set up a numerical model that can well describe the processes and take into account the different factors that influence the evolution of the movements. One of these factors is certainly the structural setting of the slab, characterized by several joints and faults; in order to better identify and detect the main joint sets affecting the study area a structural analysis was performed. Up to date, a series of scans of San Leo cliff taken in 2008 and 2011, with a Riegl Z420i were analyzed. Initially, we chose a test area, located in the east side of the cliff, in which analyses were performed using two different softwares: COLTOP 3D and Polyworks. We repeated the analysis using COLTOP for all the east wall and for a part of the north wall, including an area affected by a rock fall in 2006. In the test area we identified five sets with different dips and dip directions. The analysis of the east and north walls permitted to identify eight sets (seven plus the bedding) of discontinuities. We compared these results with previous ones from surveys taken by others authors in some areas and with some preliminary data from a traditional geological survey of the whole area. With traditional methods only a

  17. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  18. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  19. Geological interpretation and analysis of surface based, spatially referenced planetary imagery data using PRoGIS 2.0 and Pro3D.

    NASA Astrophysics Data System (ADS)

    Barnes, R.; Gupta, S.; Giordano, M.; Morley, J. G.; Muller, J. P.; Tao, Y.; Sprinks, J.; Traxler, C.; Hesina, G.; Ortner, T.; Sander, K.; Nauschnegg, B.; Paar, G.; Willner, K.; Pajdla, T.

    2015-10-01

    We apply the capabilities of the geospatial environment PRoGIS 2.0 and the real time rendering viewer PRo3D to geological analysis of NASA's Mars Exploration Rover-B (MER-B Opportunity rover) and Mars Science Laboratory (MSL Curiosity rover) datasets. Short baseline and serendipitous long baseline stereo Pancam rover imagery are used to create 3D point clouds which can be combined with super-resolution images derived from Mars Reconnaissance Orbiter HiRISE orbital data, andsuper-resolution outcrop images derived from MER Pancam, as well as hand-lens scale images for geology and outcrop characterization at all scales. Data within the PRoViDE database are presented and accessed through the PRoGIS interface. Simple geological measurement tools are implemented within the PRoGIS and PRo3D web software to accurately measure the dip and strike of bedding in outcrops, create detailed stratigraphic logs for correlation between the areas investigated, and to develop realistic 3D models for the characterization of planetary surface processes. Annotation tools are being developed to aid discussion and dissemination of the observations within the planetary science community.

  20. What spherically symmetric viscosity structure produces the same PGR as a realistic 3D Earth?

    NASA Astrophysics Data System (ADS)

    Paulson, A.; Zhong, S.; Wahr, J.

    2003-04-01

    Observations of isostatic adjustment of the earth's surface due to transient loading provide important constraints on the mantle viscosity structure. However, most studies of this response have assumed a spherically symmetric (1D) earth. This study is motivated by the following question: when a one-dimensional viscosity model is derived from post-glacial rebound (PGR) observations, how does this 1D structure correspond to the three-dimensional structure of the earth? Using the 3D spherical finite element software CitcomSVE [Zhong et al., 2002], we are able to compute the earth's response to realistic glacial loading when the earth has a truly 3D viscosity structure. The loading is provided by the ICE-3G deglaciation history [Tushingham &Peltier, 1991]. The 3D viscosity structure is constructed by first selecting a priori a radial average viscosity (for example, ( 1021 \\: {Pa \\cdot s}) in the upper mantle and (2 × 1021 \\: {Pa \\cdot s}) in the lower mantle). The lateral variations about this radial structure are derived from seismic shear-velocity tomography models by converting velocities to temperature, then temperature to viscosity. The seismic tomography models used are S20RTS [Ritsema et al., 1999] and NA00 [Van der Lee, 2002]. From the computed isostatic response, we measure typical PGR observables: relative sea level change (RSLC) and (dot{J2}). These measurements are then treated as synthetic data, and we search for 1D (radially stratified) viscosity models, forced with the same glaciation history, that will best fit these synthetic PGR observations. We find that for sites near the center of a large glacial load (e.g., southern Hudson Bay), a local average of the 3D viscosity structure provides a reasonable 1D proxy. For sites along the periphery of the glacial load (e.g., Boston), it is much more difficult to find a 1D model that can reproduce the 3D observations. We also approach the problem by running an ensemble of 1D viscosity models, and finding

  1. Mathematical structure of the three-dimensional (3D) Ising model

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given from the points of view of topology, algebra, and geometry. By analyzing the relationships among transfer matrices of the 3D Ising model, Reidemeister moves in the knot theory, Yang-Baxter and tetrahedron equations, the following facts are illustrated for the 3D Ising model. 1) The complex quaternion basis constructed for the 3D Ising model naturally represents the rotation in a (3+1)-dimensional space-time as a relativistic quantum statistical mechanics model, which is consistent with the 4-fold integrand of the partition function obtained by taking the time average. 2) A unitary transformation with a matrix that is a spin representation in 2n·l·o-space corresponds to a rotation in 2n·l·o-space, which serves to smooth all the crossings in the transfer matrices and contributes the non-trivial topological part of the partition function of the 3D Ising model. 3) A tetrahedron relationship would ensure the commutativity of the transfer matrices and the integrability of the 3D Ising model, and its existence is guaranteed by the Jordan algebra and the Jordan-von Neumann-Wigner procedures. 4) The unitary transformation for smoothing the crossings in the transfer matrices changes the wave functions by complex phases varphix, varphiy, and varphiz. The relationship with quantum field and gauge theories and the physical significance of the weight factors are discussed in detail. The conjectured exact solution is compared with numerical results, and the singularities at/near infinite temperature are inspected. The analyticity in β = 1/(kBT) of both the hard-core and the Ising models has been proved only for β > 0, not for β = 0. Thus the high-temperature series cannot serve as a standard for judging a putative exact solution of the 3D Ising model.

  2. Modelling and analysing 3D buildings with a primal/dual data structure

    NASA Astrophysics Data System (ADS)

    Boguslawski, Pawel; Gold, Christopher M.; Ledoux, Hugo

    While CityGML permits us to represent 3D city models, its use for applications where spatial analysis and/or real-time modifications are required is limited since at this moment the possibility to store topological relationships between the elements is rather limited and often not exploited. We present in this paper a new topological data structure, the dual half-edge (DHE), which permits us to represent the topology of 3D buildings (including their interiors) and of the surrounding terrain. It is based on the idea of simultaneously storing a graph in 3D space and its dual graph, and to link the two. We propose Euler-type operators for incrementally constructing 3D models (for adding individual edges, faces and volumes to the model while updating the dual structure simultaneously), and we also propose navigation operators to move from a given point to all the connected planes or polyhedra for example. The DHE also permits us to store attributes to any element. We have implemented the DHE and have tested it with different CityGML models. Our technique allows us to handle important query types, for example finding the nearest exterior exit to a given room, as in disaster management planning. As the structure is locally modifiable the model may be adapted whenever a particular pathway is no longer available. The proposed DHE structure adds significant analytic value to the increasingly popular CityGML model.

  3. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  4. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  5. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  6. The structure of Nevada`s Grant Canyon and Bacon Flat oil fields from 3-D seismic data

    SciTech Connect

    Johnson, E.H.; Zwart, D.W.

    1995-06-01

    The 20 million barrel Grant Canyon structure and its satellite feature, the one million barrel Bacon Flat field, are located at the eastern edge of Railroad Valley, Nevada. Utilizing an eleven square mile 3-D seismic survey, we have unraveled the complicated structure of the field area. The seismic data were calibrated to known geology with 21 wells drilled prior to the 1993 3-D survey, and 4 recent wells. The 3-D data cube provided vertical 2-D seismic lines every 60 feet. Horizontal slices of the data cube rendered {open_quotes}map views{close_quotes} of the structural trends. Still, the interpretation of this complex area was difficult, hampered by extreme velocity variations in the valley fill sediments that degraded data resolution and skewed the imaged structures. The Grant Canyon and Bacon Flat reservoirs are shown to be remnants of detached Devonian rocks that rest upon a northwest-trending salient of younger Paleozoic rocks. The Paleozoic rocks that form the salient are truncated to the southeast against the Troy Intrusive. Beneath the salient, the flank of the intrusive dips about 30 degrees northwest. We show Bacon Flat to be an isolated closure northwest of Grant Canyon field. However, on the south flank of the Grant Canyon reservoir, a significant oil accumulation was trapped on the down side of a normal fault, 400 feet low to the oil column of the field. This appears to be anomalous for a carbonate reservoir with extraordinary permeability, but suggests that more oil may be trapped in the area, on the flanks of producing structures.

  7. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  8. Studies of the 3D Structure of the Nucleon at JLab

    NASA Astrophysics Data System (ADS)

    Avakian, Harut

    2016-08-01

    Studies of the 3D structure of the nucleon encoded in transverse momentum dependent distribution and fragmentation functions of partons and generalized parton distributions are among the key objectives of the JLab 12 GeV upgrade and the electron ion collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  9. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  10. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  11. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  12. Research of aluminium alloy aerospace structure aperture measurement based on 3D digital speckle correlation method

    NASA Astrophysics Data System (ADS)

    Bai, Lu; Wang, Hongbo; Zhou, Jiangfan; Yang, Rong; Zhang, Hui

    2014-11-01

    In this paper, the aperture change of the aluminium alloy aerospace structure under real load is researched. Static experiments are carried on which is simulated the load environment of flight course. Compared with the traditional methods, through experiments results, it's proved that 3D digital speckle correlation method has good adaptability and precision on testing aperture change, and it can satisfy measurement on non-contact,real-time 3D deformation or stress concentration. The test results of new method is compared with the traditional method.

  13. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  14. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  15. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  16. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  17. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  18. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  19. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  20. Ground and Structure Deformation 3d Modelling with a Tin Based Property Model

    NASA Astrophysics Data System (ADS)

    TIAN, T.; Zhang, J.; Jiang, W.

    2013-12-01

    With the development of 3D( three-dimensional) modeling and visualization, more and more 3D tectonics are used to assist the daily work in Engineering Survey, in which the prediction of deformation field in strata and structure induced by underground construction is an essential part. In this research we developed a TIN (Triangulated Irregular Network) based property model for the 3D (three dimensional) visualization of ground deformation filed. By record deformation vector for each nodes, the new model can express the deformation with geometric-deformation-style by drawing each node in its new position and deformation-attribute-distribution-style by drawing each node in the color correspond with its deformation attribute at the same time. Comparing with the volume model based property model, this new property model can provide a more precise geometrical shape for structure objects. Furthermore, by recording only the deformation data of the user-interested 3d surface- such as the ground surface or the underground digging surface, the new property model can save a lot of space, which makes it possible to build the deformation filed model of a much more large scale. To construct the models of deformation filed based on TIN model, the refinement of the network is needed to increase the nodes number, which is necessary to express the deformation filed with a certain resolution. The TIN model refinement is a process of sampling the 3D deformation field values on points on the TIN surface, for which we developed a self-adapting TIN refinement method. By set the parameter of the attribute resolution, this self-adapting method refines the input geometric-expressing TIN model by adding more vertexes and triangles where the 3D deformation filed changing faster. Comparing with the even refinement method, the self-adapting method can generate a refined TIN model with nodes counted less by two thirds. Efficiency Comparison between Self-adapting Refinement Method and Even

  1. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  2. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  3. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

  4. 3D seismic geomorphology and geologic controls on gas hydrate accumulation mechanism in the Miyazaki-oki forearc basin, Japan

    NASA Astrophysics Data System (ADS)

    Komatsu, Y.; Kobayashi, T.; Fujii, T.

    2015-12-01

    The stratigraphy of the Miyazaki-oki forearc basin along the Southwest Japan Arc comprises the early Miocene to early Pleistocene Miyazaki Group and the Hyuganada Group. These groups comprise sediments (up to 5000 m) deposited in deep marine to shallow marine environments. Based on characteristics of well data outside seismic exploration area and stratigraphy of land areas, the Miyazaki Group was divided into four seismic units and the Hyuganada Group was divided into two seismic units. In this area, bottom-simulating reflectors (BSRs) have been widely observed and considered as representing lower boundaries of methane-hydrate-bearing deposits. However, the gas hydrate accumulation mechanism for this area is not yet well understood. We show the relation between sandy sediment distribution identified from the 3D seismic geomorphological analysis and methane hydrate occurrence to identify the accumulation mechanism. A submarine fan system was subdivided into four seismic facies: Submarine canyon complexes; Leveed channel complexes; Submarine fan complexes; Mass transport complexes (MTD). Depositional systems of target layers are characterized by a transition from submarine fan deposits (Miyazaki Group) to channel-levee deposits and MTD (Hyuganada Group). This transition of depositional environments is strongly influenced by global tectonics since early Miocene in the Southwest Japan Arc. A part of channel-fill located around structural wing and middle fan deposits above the BSR is inferred as sediments intercalated with sandy layers. We consider that these deposits contain methane hydrate because the sandy sediment distribution approximately coincides with a high-velocity zone as an indicator of gas hydrate. The comparison of the areal extent of the seismic facies and the mapped structural configuration, suggest that the gas hydrate accumulation represent combination structural-stratigraphic trap.

  5. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  6. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  7. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  8. Analysis of the rupture process of the 1995 Kobe earthquake using a 3D velocity structure

    NASA Astrophysics Data System (ADS)

    Guo, Yujia; Koketsu, Kazuki; Ohno, Taichi

    2013-12-01

    A notable feature of the 1995 Kobe (Hyogo-ken Nanbu) earthquake is that violent ground motions occurred in a narrow zone. Previous studies have shown that the origin of such motions can be explained by the 3D velocity structure in this zone. This indicates not only that the 3D velocity structure significantly affects strong ground motions, but also that we should consider its effects in order to determine accurately the rupture process of the earthquake. Therefore, we have performed a joint source inversion of strong-motion, geodetic, and teleseismic data, where 3D Green's functions were calculated for strong-motion and geodetic data in the Osaka basin. Our source model estimates the total seismic moment to be about 2.1 × 1019 N m and the maximum slip reaches 2.9 m near the hypocenter. Although the locations of large slips are similar to those reported by Yoshida et al. (1996), there are quantitative differences between our results and their results due to the differences between the 3D and 1D Green's functions. We have also confirmed that our source model realized a better fit to the strong motion observations, and a similar fit as Yoshida et al. (1996) to the observed static displacements.

  9. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  10. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

  11. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  12. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  13. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

  14. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  15. Finding the displacement of wood structure in heritage building by 3D laser scanner

    NASA Astrophysics Data System (ADS)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  16. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  17. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  18. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  19. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  20. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  1. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  2. Sequence-based identification of 3D structural modules in RNA with RMDetect.

    PubMed

    Cruz, José Almeida; Westhof, Eric

    2011-06-01

    Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data. PMID:21552257

  3. The geothermal field below the city of Berlin, Germany: Results from structurally and parametrically improved 3D Models

    NASA Astrophysics Data System (ADS)

    Frick, Maximilian; Sippel, Judith; Cacace, Mauro; Scheck-Wenderoth, Magdalena

    2016-04-01

    The goal of this study was to quantify the influence of the geological structure and geophysical parametrization of model units on the geothermal field as calculated by 3D numerical simulations of coupled fluid and heat transport for the subsurface of Berlin, Germany. The study area is located in the Northeast German Basin which is filled with several kilometers of sediments. This sedimentary infill includes the clastic sedimentary units Middle Buntsandstein and Sedimentary Rotliegend which are of particular interest for geothermal exploration. Previous studies conducted in the Northeast German Basin have already shown the geometries and properties of the geological units majorly control the distribution of subsurface temperatures. In this study we followed a two-step approach, where we first improved an existing structural model by integrating newly available 57 geological cross-sections, well data and deep seismics (down to ~4 km). Secondly, we performed a sensitivity analysis investigating the effects of varying physical fluid and rock properties on the subsurface temperature field. The results of this study show, that the structural configuration of model units exerts the highest influence on the geothermal field (up to ± 23 K at 1000 m below sea level). Here, the Rupelian clay aquitard, displaying a heterogeneous thickness distribution, locally characterized by hydrogeological windows (i.e. domains of no thickness) enabling intra-aquifer groundwater circulation has been identified as major controlling factor. The new structural configuration of this unit (more continuous, less numerous hydrogeological windows) also leads to a reduction of the influence of different boundary conditions and heat transport mechanisms considered. Additionally, the models results show that calculated temperatures highly depend on geophysical properties of model units whereas the hydraulic conductivity of the Cenozoic succession was identified as most dominant, leading to changes

  4. Low-cost structured-light based 3D capture system design

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  5. Experimentation of structured light and stereo vision for underwater 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Bruno, F.; Bianco, G.; Muzzupappa, M.; Barone, S.; Razionale, A. V.

    Current research on underwater 3D imaging methods is mainly addressing long range applications like seafloor mapping or surveys of archeological sites and shipwrecks. Recently, there is an increasing need for more accessible and precise close-range 3D acquisition technologies in some application fields like, for example, monitoring the growth of coral reefs or reconstructing underwater archaeological pieces that in most cases cannot be recovered from the seabed. This paper presents the first results of a research project that aims to investigate the possibility of using active optical techniques for the whole-field 3D reconstructions in an underwater environment. In this work we have tested an optical technique, frequently used for in air acquisition, based on the projection of structured lighting patterns acquired by a stereo vision system. We describe the experimental setup used for the underwater tests, which were conducted in a water tank with different turbidity conditions. The tests have evidenced that the quality of 3D reconstruction is acceptable even with high turbidity values, despite the heavy presence of scattering and absorption effects.

  6. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

  7. Determination and validation of mTOR kinase-domain 3D structure by homology modeling

    PubMed Central

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525

  8. Utilizing in-situ resources and 3D printing structures for a manned Mars mission

    NASA Astrophysics Data System (ADS)

    Kading, Benjamin; Straub, Jeremy

    2015-02-01

    This paper presents a manned Mars mission, which is based on the use of in-situ resources for the fabrication of structures. First, it provides an overview of the two-phase mission. In phase one, robotic construction units prepare a functional base for phase-two human habitation. Then, it describes a set of prospective structures that can be created utilizing additive manufacturing (commonly known as 3D printing) techniques and in situ materials. Next, the technological advancements required to allow this type of mission are considered and their feasibility is discussed. Specific focus is given to the topics of basalt 3D printing and the maintenance of the pressure environment. The process of the construction of the base is also discussed. Finally the proposed approach is analyzed through comparison to prior missions, before concluding.

  9. Topology optimization of 3D structures with design-dependent loads

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Liu, Shu-Tian; Zhang, Xiong

    2010-10-01

    Topology optimization of continuum structures with design-dependent loads has long been a challenge. In this paper, the topology optimization of 3D structures subjected to design-dependent loads is investigated. A boundary search scheme is proposed for 3D problems, by means of which the load surface can be identified effectively and efficiently, and the difficulties arising in other approaches can be overcome. The load surfaces are made up of the boundaries of finite elements and the loads can be directly applied to corresponding element nodes, which leads to great convenience in the application of this method. Finally, the effectiveness and efficiency of the proposed method is validated by several numerical examples.

  10. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    PubMed Central

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  11. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  12. 3D reconstruction of internal structure of animal body using near-infrared light

    NASA Astrophysics Data System (ADS)

    Tran, Trung Nghia; Yamamoto, Kohei; Namita, Takeshi; Kato, Yuji; Shimizu, Koichi

    2014-03-01

    To realize three-dimensional (3D) optical imaging of the internal structure of animal body, we have developed a new technique to reconstruct CT images from two-dimensional (2D) transillumination images. In transillumination imaging, the image is blurred due to the strong scattering in the tissue. We had developed a scattering suppression technique using the point spread function (PSF) for a fluorescent light source in the body. In this study, we have newly proposed a technique to apply this PSF for a light source to the image of unknown light-absorbing structure. The effectiveness of the proposed technique was examined in the experiments with a model phantom and a mouse. In the phantom experiment, the absorbers were placed in the tissue-equivalent medium to simulate the light-absorbing organs in mouse body. Near-infrared light was illuminated from one side of the phantom and the image was recorded with CMOS camera from another side. Using the proposed techniques, the scattering effect was efficiently suppressed and the absorbing structure can be visualized in the 2D transillumination image. Using the 2D images obtained in many different orientations, we could reconstruct the 3D image. In the mouse experiment, an anesthetized mouse was held in an acrylic cylindrical holder. We can visualize the internal organs such as kidneys through mouse's abdomen using the proposed technique. The 3D image of the kidneys and a part of the liver were reconstructed. Through these experimental studies, the feasibility of practical 3D imaging of the internal light-absorbing structure of a small animal was verified.

  13. A theoretical study of the structure and stability of borohydride on 3d transition metals

    NASA Astrophysics Data System (ADS)

    Arevalo, Ryan Lacdao; Escaño, Mary Clare Sison; Gyenge, Elod; Kasai, Hideaki

    2012-12-01

    The adsorption of borohydride on 3d transition metals (Cr, Mn, Fe, Co, Ni and Cu) was studied using first principles calculations within spin-polarized density functional theory. Magnetic effect on the stability of borohydride is noted. Molecular adsorption is favorable on Co, Ni and Cu, which is characterized by the strong s-dzz hybridization of the adsorbate-substrate states. Dissociated adsorption structure yielding one or two H adatom fragments on the surface is observed for Cr, Mn and Fe.

  14. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  15. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  16. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

  17. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

    Zhou, Changjun; Hou, Caixia; Zhang, Qiang; Wei, Xiaopeng

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  18. Segmentation of bone structures in 3D CT images based on continuous max-flow optimization

    NASA Astrophysics Data System (ADS)

    Pérez-Carrasco, J. A.; Acha-Piñero, B.; Serrano, C.

    2015-03-01

    In this paper an algorithm to carry out the automatic segmentation of bone structures in 3D CT images has been implemented. Automatic segmentation of bone structures is of special interest for radiologists and surgeons to analyze bone diseases or to plan some surgical interventions. This task is very complicated as bones usually present intensities overlapping with those of surrounding tissues. This overlapping is mainly due to the composition of bones and to the presence of some diseases such as Osteoarthritis, Osteoporosis, etc. Moreover, segmentation of bone structures is a very time-consuming task due to the 3D essence of the bones. Usually, this segmentation is implemented manually or with algorithms using simple techniques such as thresholding and thus providing bad results. In this paper gray information and 3D statistical information have been combined to be used as input to a continuous max-flow algorithm. Twenty CT images have been tested and different coefficients have been computed to assess the performance of our implementation. Dice and Sensitivity values above 0.91 and 0.97 respectively were obtained. A comparison with Level Sets and thresholding techniques has been carried out and our results outperformed them in terms of accuracy.

  19. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

    PubMed Central

    Nadzirin, Nurul; Gardiner, Eleanor J.; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

    2012-01-01

    Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/. PMID:22573174

  20. Integration of nano-scale components and supports in micromachined 3D silicon structures

    NASA Astrophysics Data System (ADS)

    Song, J.; Azimi, S.; Y Dang, Z.; Breese, M. B. H.

    2014-04-01

    We have developed a process for the three-dimensional (3D) machining of p-type silicon on a micro- and nano-scale using high-energy ion beam irradiation with one or more energies and fluences, followed by electrochemical anodization in hydrofluoric acid. We present a study of the dependence of our fabricated structures on irradiating ion energies, fluences, geometries and wafer resistivity. All these factors determine whether the micro- and nano-scale features are properly connected to the supports in the 3D silicon structures. If wrongly chosen, any of these factors may cause a breakage at the connection through localized over-etching. Under optimum irradiation and anodization conditions, free-standing patterned membranes can be fabricated with feature dimensions of 100 nm over areas of many square millimeters. This investigation is based on silicon structures but is relevant to any electro-assisted etching process for 3D fabrication, paving the way for achieving free-standing silicon photonics, mechanical resonators and micro-/nano-electromechanical systems.

  1. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  2. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  3. Novel 3D bismuth-based coordination polymers: Synthesis, structure, and second harmonic generation properties

    SciTech Connect

    Wibowo, Arief C.; Smith, Mark D.; Yeon, Jeongho; Halasyamani, P. Shiv; Loye, Hans-Conrad zur

    2012-11-15

    Two new 3D bismuth containing coordination polymers are reported along with their single crystal structures and SHG properties. Compound 1: Bi{sub 2}O{sub 2}(pydc) (pydc=pyridine-2, 5-dicarboxylate), crystallizes in the monoclinic, polar space group, P2{sub 1} (a=9.6479(9) A, b=4.2349(4) A, c=11.9615(11) A, {beta}=109.587(1) Degree-Sign ), which contains Bi{sub 2}O{sub 2} chains that are connected into a 3D structure via the pydc ligands. Compound 2: Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (1R3S cam=1R3S-camphoric acid) crystallizes in the monoclinic, polar space group, P2{sub 1} (a=19.0855(7) A, b=13.7706(5) A, c=19.2429(7) A, {beta}=90.701(1) Degree-Sign ) and is a true 3D coordination polymer. These are two example of SHG compounds prepared using unsymmetric ligands (compound 1) or chiral ligands (compound 2), together with metals that often exhibit stereochemically-active lone pairs, such as Bi{sup 3+}, a synthetic approach that resulted in polar, non-centrosymmetric, 3D metal-organic coordination polymer. - Graphical Abstract: Structures of two new, polar, 3D Bismuth(III)-based coordination polymers: Bi{sub 2}O{sub 2}(pydc) (compound 1), and Bi{sub 4}Na{sub 4}(1R3S-cam){sub 8}(EtOH){sub 3.1}(H{sub 2}O){sub 3.4} (compound 2). Highlights: Black-Right-Pointing-Pointer New, polar, 3D Bismuth(III)-based coordination polymers. Black-Right-Pointing-Pointer First polar bismuth-based coordination polymers synthesized via a 'hybrid' strategy. Black-Right-Pointing-Pointer Combination of stereochemically-active lone pairs and unsymmetrical or chiral ligands. Black-Right-Pointing-Pointer Synthesis of class C-SHG materials based on Kurtz-Perry categories.

  4. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  5. Clumped Isotope Thermometry of Geologic Methane (13CH3D) using Tunable Laser Mid-Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ono, S.; Zahniser, M. S.; McManus, J. B.; Nelson, D. D.

    2013-12-01

    Methane is both an alternative energy source as well as a significant greenhouse gas, and holds the potential for rapid release to the atmosphere, possibly triggering abrupt climate change in the past and in the future. The majority of methane on the Earth is biogenic, originating from microbial methanogenesis, or thermogenic sourced from previously formed biogenic organic materials. Methane can be also produced abiogenically during serpentinization and even mantle-sourced methane has been implicated. Carbon (13C/12C) and hydrogen (D/H) isotope ratios of methane and associated short chain hydrocarbons provide critical information about the abiogenic/biogenic origin of methane but data can be inconclusive. We have developed and tested a Tunable Infrared Laser Direct Absorption Spectroscopy (TILDAS) Instrument to be used for precise measurements of the abundance of doubly isotope-substituted methane (13CH3D). The TILDAS instrument measures direct absorption in the mid-infrared (~ 8 μm) region using continuous wave quantum cascade laser combined with a 76 m pathlength astigmatic absorption cell. Initial test result indicates the precision for 13CH4, 12CH3D and 13CH3D for 0.2 ‰ or better for comparison between two reference gases. Accuracy of the methods for δ13C and δD is evaluated by comparing measurements by conventional isotope ratio mass spectrometry. Calibration of clumped isotope scale (δ13CH3D) is underway using methane produced at various temperatures. Following an isotope exchange reaction (13CH4 + 12CH3D ↔ 13CH3D + 12CH4), precise measurements of 13CH3D abundance is expected to provide new and critical information about the temperature at which methane was formed (or thermally equilibrated). Biogenic origin becomes highly unlikely, for example, if the estimated temperature is higher than 120°C, i.e., current high-temperature limit of microbial methanogenesis. Although significant questions remain regarding isotope exchange kinetics, and clumped

  6. Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.

    PubMed

    Mrozek, Dariusz; Brożek, Miłosz; Małysiak-Mrozek, Bożena

    2014-02-01

    Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. However, the computational complexity of this process means that it is constantly necessary to search for new methods that can perform such a process faster and more efficiently. Finding molecular substructures that complex protein structures have in common is still a challenging task, especially when entire databases containing tens or even hundreds of thousands of protein structures must be scanned. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) can perform many time-consuming and computationally demanding processes much more quickly than a classical CPU can. In this paper, we describe the GPU-based implementation of the CASSERT algorithm for 3D protein structure similarity searching. This algorithm is based on the two-phase alignment of protein structures when matching fragments of the compared proteins. The GPU (GeForce GTX 560Ti: 384 cores, 2GB RAM) implementation of CASSERT ("GPU-CASSERT") parallelizes both alignment phases and yields an average 180-fold increase in speed over its CPU-based, single-core implementation on an Intel Xeon E5620 (2.40GHz, 4 cores). In this paper, we show that massive parallelization of the 3D structure similarity search process on many-core GPU devices can reduce the execution time of the process, allowing it to be performed in real time. GPU-CASSERT is available at: http://zti.polsl.pl/dmrozek/science/gpucassert/cassert.htm. PMID:24481593

  7. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

    PubMed Central

    Dai, Chao; Li, Wenyuan; Tjong, Harianto; Hao, Shengli; Zhou, Yonggang; Li, Qingjiao; Chen, Lin; Zhu, Bing; Alber, Frank; Jasmine Zhou, Xianghong

    2016-01-01

    Three-dimensional (3D) genome structures vary from cell to cell even in an isogenic sample. Unlike protein structures, genome structures are highly plastic, posing a significant challenge for structure-function mapping. Here we report an approach to comprehensively identify 3D chromatin clusters that each occurs frequently across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data. Applying our method to a population of genome structures (at the macrodomain resolution) of lymphoblastoid cells, we identify an atlas of stable inter-chromosomal chromatin clusters. A large number of these clusters are enriched in binding of specific regulatory factors and are therefore defined as ‘Regulatory Communities.' We reveal two major factors, centromere clustering and transcription factor binding, which significantly stabilize such communities. Finally, we show that the regulatory communities differ substantially from cell to cell, indicating that expression variability could be impacted by genome structures. PMID:27240697

  8. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers.

    PubMed

    Mao, Yiqi; Yu, Kai; Isakov, Michael S; Wu, Jiangtao; Dunn, Martin L; Jerry Qi, H

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  9. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    PubMed Central

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-01-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations. PMID:26346202

  10. Sequential Self-Folding Structures by 3D Printed Digital Shape Memory Polymers

    NASA Astrophysics Data System (ADS)

    Mao, Yiqi; Yu, Kai; Isakov, Michael S.; Wu, Jiangtao; Dunn, Martin L.; Jerry Qi, H.

    2015-09-01

    Folding is ubiquitous in nature with examples ranging from the formation of cellular components to winged insects. It finds technological applications including packaging of solar cells and space structures, deployable biomedical devices, and self-assembling robots and airbags. Here we demonstrate sequential self-folding structures realized by thermal activation of spatially-variable patterns that are 3D printed with digital shape memory polymers, which are digital materials with different shape memory behaviors. The time-dependent behavior of each polymer allows the temporal sequencing of activation when the structure is subjected to a uniform temperature. This is demonstrated via a series of 3D printed structures that respond rapidly to a thermal stimulus, and self-fold to specified shapes in controlled shape changing sequences. Measurements of the spatial and temporal nature of self-folding structures are in good agreement with the companion finite element simulations. A simplified reduced-order model is also developed to rapidly and accurately describe the self-folding physics. An important aspect of self-folding is the management of self-collisions, where different portions of the folding structure contact and then block further folding. A metric is developed to predict collisions and is used together with the reduced-order model to design self-folding structures that lock themselves into stable desired configurations.

  11. Combination of photogrammetric and geoelectric methods to assess 3d structures associated to natural hazards

    NASA Astrophysics Data System (ADS)

    Fargier, Yannick; Dore, Ludovic; Antoine, Raphael; Palma Lopes, Sérgio; Fauchard, Cyrille

    2016-04-01

    The extraction of subsurface materials is a key element for the economy of a nation. However, natural degradation of underground quarries is a major issue from an economic and public safety point of view. Consequently, the quarries stakeholders require relevant tools to define hazards associated to these structures. Safety assessment methods of underground quarries are recent and mainly based on rock physical properties. This kind of method leads to a certain homogeneity assumption of pillar internal properties that can cause an underestimation of the risk. Electrical Resistivity Imaging (ERI) is a widely used method that possesses two advantages to overcome this limitation. The first is to provide a qualitative understanding for the detection and monitoring of anomalies in the pillar body (e.g. faults). The second is to provide a quantitative description of the electrical resistivity distribution inside the pillar. This quantitative description can be interpreted with constitutive laws to help decision support (water content decreases the mechanical resistance of a chalk). However, conventional 2D and 3D Imaging techniques are usually applied to flat surface surveys or to surfaces with moderate topography. A 3D inversion of more complex media (case of the pillar) requires a full consideration of the geometry that was never taken into account before. The Photogrammetric technique presents a cost effective solution to obtain an accurate description of the external geometry of a complex media. However, this method has never been fully coupled with a geophysical method to enhance/improve the inversion process. Consequently we developed a complete procedure showing that photogrammetric and ERI tools can be efficiently combined to assess a complex 3D structure. This procedure includes in a first part a photogrammetric survey, a processing stage with an open source software and a post-processing stage finalizing a 3D surface model. The second part necessitates the

  12. 3D measurement method based on combined temporal encoding structured light

    NASA Astrophysics Data System (ADS)

    Yu, Xiaoyang; Wang, Yang; Yu, Shuang; Cheng, Hao; Sun, Xiaoming; Yu, Shuchun; Chen, Deyun

    2013-10-01

    Three-dimensional (3D) vision measurement technology based on encoding structured light plays an important role and has become the main development trend in the field of 3D non-contact measurement. However, how to synthetically improve measurement speed, accuracy and sampling density is still a difficult problem. Thus in the present work, a novel 3D measurement method based on temporal encoding structured light by combining trapezoidal phase-shifting pattern and cyclic code pattern is proposed. Due to trapezoidal phase-shifting has the advantages of high sampling density and high-speed, the proposed method can maintain these advantages by using cyclic code to expand the range of trapezoidal phase-shifting. In addition, the correction scheme is designed to solve the problem of cycle dislocation. Finally, simulation experimental platform is built with 3ds max and MATLAB. Experimental analyses and results show that, the maximal error is less than 3 mm in the range from 400 mm to 1100 mm, cycle dislocation correction has a good effect.

  13. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  14. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    PubMed

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-01

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated. PMID:23558903

  15. Direct observation in 3d of structural crossover in binary hard sphere mixtures

    NASA Astrophysics Data System (ADS)

    Statt, Antonia; Pinchaipat, Rattachai; Turci, Francesco; Evans, Robert; Royall, C. Patrick

    2016-04-01

    For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon et al., J. Chem. Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl et al., Phys. Rev. Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

  16. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  17. Shape optimization of 3D continuum structures via force approximation techniques

    NASA Technical Reports Server (NTRS)

    Vanderplaats, Garret N.; Kodiyalam, Srinivas

    1988-01-01

    The existing need to develop methods whereby the shape design efficiency can be improved through the use of high quality approximation methods is addressed. An efficient approximation method for stress constraints in 3D shape design problems is proposed based on expanding the nodal forces in Taylor series with respect to shape variations. The significance of this new method is shown through elementary beam theory calculations and via numerical computations using 3D solid finite elements. Numerical examples including the classical cantilever beam structure and realistic automotive parts like the engine connecting rod are designed for optimum shape using the proposed method. The numerical results obtained from these methods are compared with other published results, to assess the efficiency and the convergence rate of the proposed method.

  18. The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  19. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

  20. 3D visualization of deformation structures and potential fluid pathways at the Grimsel Test Site

    NASA Astrophysics Data System (ADS)

    Schneeberger, Raphael; Kober, Florian; Berger, Alfons; Spillmann, Thomas; Herwegh, Marco

    2015-04-01

    Knowledge on the ability of fluids to infiltrate subsurface rocks is of major importance for underground constructions, geothermal or radioactive waste disposal projects. In this study, we focus on the characterization of water infiltration pathways, their 3D geometries and origins. Based on surface and subsurface mapping in combination with drill core data, we developed by the use of MoveTM (Midland Valley Exploration Ltd.) a 3D structural model of the Grimsel Test Site (GTS). GTS is an underground laboratory operated by NAGRA, the Swiss organisation responsible for the management of nuclear waste. It is located within a suite of post-Variscan magmatic bodies comprising former granitic and granodioritic melts, which are dissected by mafic and aplitic dikes. During Alpine orogeny, the suite was tectonically overprinted within two stages of ductile deformation (Wehrens et al., in prep.) followed by brittle overprint of some of the shear zones during the retrograde exhumation history. It is this brittle deformation, which controls today's water infiltration network. However, the associated fractures, cataclasites and fault gouges are controlled themselves by aforementioned pre-existing mechanical discontinuities, whose origin ranges back as far as to the magmatic stage. For example, two sets of vertically oriented mafic dikes (E-W and NW-SE striking) and compositional heterogeneities induced by magmatic segregation processes in the plutonic host rocks served as nucleation sites for Alpine strain localization. Subsequently, NE-SW, E-W and NW-SE striking ductile shear zones were formed, in combination with high temperature fracturing while dissecting the host rocks in a complex 3D pattern (Wehrens et al, in prep.). Whether the ductile shear zones have been subjected to brittle reactivation and can serve as infiltration pathways or not, depends strongly on their orientations with respect to the principal stress field. Especially where deformation structures intersect

  1. Reconstruction of 3D structure using stochastic methods: morphology and transport properties

    NASA Astrophysics Data System (ADS)

    Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena

    2013-04-01

    One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions

  2. Loading mode dependent effective properties of octet-truss lattice structures using 3D-printing

    NASA Astrophysics Data System (ADS)

    Challapalli, Adithya

    Cellular materials, often called lattice materials, are increasingly receiving attention for their ultralight structures with high specific strength, excellent impact absorption, acoustic insulation, heat dissipation media and compact heat exchangers. In alignment with emerging additive manufacturing (AM) technology, realization of the structural applications of the lattice materials appears to be becoming faster. Considering the direction dependent material properties of the products with AM, by directionally dependent printing resolution, effective moduli of lattice structures appear to be directionally dependent. In this paper, a constitutive model of a lattice structure, which is an octet-truss with a base material having an orthotropic material property considering AM is developed. In a case study, polyjet based 3D printing material having an orthotropic property with a 9% difference in the principal direction provides difference in the axial and shear moduli in the octet-truss by 2.3 and 4.6%. Experimental validation for the effective properties of a 3D printed octet-truss is done for uniaxial tension and compression test. The theoretical value based on the micro-buckling of truss member are used to estimate the failure strength. Modulus value appears a little overestimate compared with the experiment. Finite element (FE) simulations for uniaxial compression and tension of octettruss lattice materials are conducted. New effective properties for the octet-truss lattice structure are developed considering the observed behavior of the octet-truss structure under macroscopic compression and tension trough simulations.

  3. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

    PubMed Central

    Gouet, Patrice; Robert, Xavier; Courcelle, Emmanuel

    2003-01-01

    The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Cα trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript. PMID:12824317

  4. The "lnc" between 3D chromatin structure and X chromosome inactivation.

    PubMed

    Pandya-Jones, Amy; Plath, Kathrin

    2016-08-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilitates the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  5. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    NASA Astrophysics Data System (ADS)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

  6. The “lnc” between 3D Chromatin Structure and X Chromosome Inactivation

    PubMed Central

    Pandya-Jones, Amy; Plath, Kathrin

    2016-01-01

    The long non-coding RNA Xist directs a remarkable instance of developmentally regulated, epigenetic change known as X Chromosome Inactivation (XCI). By spreading in cis across the X chromosome from which it is expressed, Xist RNA facilities the creation of a heritably silent, heterochromatic nuclear territory that displays a three-dimensional structure distinct from that of the active X chromosome. How Xist RNA attaches to and propagates across a chromosome and its influence over the three-dimensional (3D) structure of the inactive X are aspects of XCI that have remained largely unclear. Here, we discuss studies that have made significant contributions towards answering these open questions. PMID:27062886

  7. Geologic and structural map of eastern Asia

    SciTech Connect

    Letouzey, J.; Sage, L.

    1986-07-01

    A synthesis of the onshore and offshore geologic data of eastern Asia, prepared by the Institut Francais du Petrole (IFP), has allowed the construction of geologic and structural maps for this region. These maps include three color sheets (scale = 1:2.5 million) and three plates of geologic and structural cross sections. Located between lat. 4/sup 0/ and 35/sup 0/N, and long. 106/sup 0/ and 132/sup 0/E, the maps cover the following geographic areas: East and South China Sea, Sulu Sea, West Philippine basin and onshore neighboring terrains, Kyushu and Ryukyu Islands, the China margin, Taiwan Island, Vietnam, North West Borneo, and the Philippines. The maps synthesize seismic interpretations, oil well data, geologic work in south Japan, Taiwan, Borneo, and the Philippines, and recent data published between 1976 and 1985. Twenty-four geologic cross sections (scale = 1:1.25 million, vertical exaggeration x 6) intersect ocean margins, important basins, and the different structural domains. They are based on seismic profiles, well data, and available onshore and offshore geologic data. These cross sections show basement composition and structures, different tectonic and sedimentary domains, and the structure and thickness of different sedimentary deposits (such as age, unconformities, and geologic structures). Maps and cross sections will be published in early 1987.

  8. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  9. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  10. Learning the 3-D structure of objects from 2-D views depends on shape, not format.

    PubMed

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-05-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  11. Color influence on accuracy of 3D scanners based on structured light

    NASA Astrophysics Data System (ADS)

    Voisin, Sophie; Page, David L.; Foufou, Sebti; Truchetet, Frédéric; Abidi, Mongi A.

    2006-02-01

    The characterization of commercial 3D scanners allows acquiring precise and useful data. The accuracy of range and, more recently, color for 3D scanners is usually studied separately, but when the 3D scanner is based on structured light with a color coding pattern, color influence on range accuracy should be investigated. The commercial product that we have tested has the particularity that it can acquire data under ambient light instead of a controlled environment as it is with most available scanners. Therefore, based on related work in the literature and on experiments we have done on a variety of standard illuminants, we have designed an interesting setup to control illuminant interference. Basically, the setup consists of acquiring the well-known Macbeth ColorChecker under a controlled environment and also ambient daylight. The results have shown variations with respect to the color. We have performed several statistical studies to show how the range results evolve with respect to the RGB and the HSV channels. In addition, a systematic noise error has also been identified. This noise depends on the object color. A subset of colors shows strong noise errors while other colors have minimal or even no systematic error under the same illuminant.

  12. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visu