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

Science.gov (United States)

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

TLS-Based Feature Extraction and 3D Modeling for Arch Structures

Directory of Open Access Journals (Sweden)

Xiangyang Xu

2017-01-01

Full Text Available Terrestrial laser scanning (TLS technology is one of the most efficient and accurate tools for 3D measurement which can reveal surface-based characteristics of objects with the aid of computer vision and programming. Thus, it plays an increasingly important role in deformation monitoring and analysis. Automatic data extraction and high efficiency and accuracy modeling from scattered point clouds are challenging issues during the TLS data processing. This paper presents a data extraction method considering the partial and statistical distribution of the point clouds scanned, called the window-neighborhood method. Based on the point clouds extracted, 3D modeling of the boundary of an arched structure was carried out. The ideal modeling strategy should be fast, accurate, and less complex regarding its application to large amounts of data. The paper discusses the accuracy of fittings in four cases between whole curve, segmentation, polynomial, and B-spline. A similar number of parameters was set for polynomial and B-spline because the number of unknown parameters is essential for the accuracy of the fittings. The uncertainties of the scanned raw point clouds and the modeling are discussed. This process is considered a prerequisite step for 3D deformation analysis with TLS.

Gis-Based Smart Cartography Using 3d Modeling

Science.gov (United States)

Malinverni, E. S.; Tassetti, A. N.

2013-08-01

3D City Models have evolved to be important tools for urban decision processes and information systems, especially in planning, simulation, analysis, documentation and heritage management. On the other hand existing and in use numerical cartography is often not suitable to be used in GIS because not geometrically and topologically correctly structured. The research aim is to 3D structure and organize a numeric cartography for GIS and turn it into CityGML standardized features. The work is framed around a first phase of methodological analysis aimed to underline which existing standard (like ISO and OGC rules) can be used to improve the quality requirement of a cartographic structure. Subsequently, from this technical specifics, it has been investigated the translation in formal contents, using an owner interchange software (SketchUp), to support some guide lines implementations to generate a GIS3D structured in GML3. It has been therefore predisposed a test three-dimensional numerical cartography (scale 1:500, generated from range data captured by 3D laser scanner), tested on its quality according to the previous standard and edited when and where necessary. Cad files and shapefiles are converted into a final 3D model (Google SketchUp model) and then exported into a 3D city model (CityGML LoD1/LoD2). The GIS3D structure has been managed in a GIS environment to run further spatial analysis and energy performance estimate, not achievable in a 2D environment. In particular geometrical building parameters (footprint, volume etc.) are computed and building envelop thermal characteristics are derived from. Lastly, a simulation is carried out to deal with asbestos and home renovating charges and show how the built 3D city model can support municipal managers with risk diagnosis of the present situation and development of strategies for a sustainable redevelop.

The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

Energy Technology Data Exchange (ETDEWEB)

Blecic, Jasmina; Dobbs-Dixon, Ian [NYU Abu Dhabi, Abu Dhabi (United Arab Emirates); Greene, Thomas, E-mail: jasmina@nyu.edu [NASA Ames Research Center, Space Sciece and Astrobiology Division, M.S. 245-6, Moffett Field, CA 94035 (United States)

2017-10-20

Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer , the Hubble Space Telescope ( HST ), and the James Web Space Telescope ( JWST ) bandpasses, covering the wavelength range between 1 and 11 μ m where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailed comparisons between the temperature–pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and

The Implications of 3D Thermal Structure on 1D Atmospheric Retrieval

Science.gov (United States)

Blecic, Jasmina; Dobbs-Dixon, Ian; Greene, Thomas

2017-10-01

Using the atmospheric structure from a 3D global radiation-hydrodynamic simulation of HD 189733b and the open-source Bayesian Atmospheric Radiative Transfer (BART) code, we investigate the difference between the secondary-eclipse temperature structure produced with a 3D simulation and the best-fit 1D retrieved model. Synthetic data are generated by integrating the 3D models over the Spitzer, the Hubble Space Telescope (HST), and the James Web Space Telescope (JWST) bandpasses, covering the wavelength range between 1 and 11 μm where most spectroscopically active species have pronounced features. Using the data from different observing instruments, we present detailed comparisons between the temperature-pressure profiles recovered by BART and those from the 3D simulations. We calculate several averages of the 3D thermal structure and explore which particular thermal profile matches the retrieved temperature structure. We implement two temperature parameterizations that are commonly used in retrieval to investigate different thermal profile shapes. To assess which part of the thermal structure is best constrained by the data, we generate contribution functions for our theoretical model and each of our retrieved models. Our conclusions are strongly affected by the spectral resolution of the instruments included, their wavelength coverage, and the number of data points combined. We also see some limitations in each of the temperature parametrizations, as they are not able to fully match the complex curvatures that are usually produced in hydrodynamic simulations. The results show that our 1D retrieval is recovering a temperature and pressure profile that most closely matches the arithmetic average of the 3D thermal structure. When we use a higher resolution, more data points, and a parametrized temperature profile that allows more flexibility in the middle part of the atmosphere, we find a better match between the retrieved temperature and pressure profile and the

Static/dynamic fluid-structure interaction analysis for 3-D rotary blade model

International Nuclear Information System (INIS)

Kim, Dong Hyun; Kim, Yu Sung; Kim, Dong Man; Park, Kang Kyun

2009-01-01

In this study, static/dynamic fluid-structure interaction analyses have been conducted for a 3D rotary blade model like a turbo-machinery or wind turbine blade. Advanced computational analysis system based on Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD) has been developed in order to investigate detailed dynamic responses of rotary type models. Fluid domains are modeled using the computational grid system with local grid deforming techniques. Reynolds-averaged Navier-Stokes equations with various turbulence model are solved for unsteady flow problems of the rotating blade model. Detailed static/dynamic responses and instantaneous pressure contours on the blade surfaces considering flow-separation effects are presented to show the multi-physical phenomenon of the rotating blades.

Extracting 3D layout from a single image using global image structures.

Science.gov (United States)

Lou, Zhongyu; Gevers, Theo; Hu, Ninghang

2015-10-01

Extracting the pixel-level 3D layout from a single image is important for different applications, such as object localization, image, and video categorization. Traditionally, the 3D layout is derived by solving a pixel-level classification problem. However, the image-level 3D structure can be very beneficial for extracting pixel-level 3D layout since it implies the way how pixels in the image are organized. In this paper, we propose an approach that first predicts the global image structure, and then we use the global structure for fine-grained pixel-level 3D layout extraction. In particular, image features are extracted based on multiple layout templates. We then learn a discriminative model for classifying the global layout at the image-level. Using latent variables, we implicitly model the sublevel semantics of the image, which enrich the expressiveness of our model. After the image-level structure is obtained, it is used as the prior knowledge to infer pixel-wise 3D layout. Experiments show that the results of our model outperform the state-of-the-art methods by 11.7% for 3D structure classification. Moreover, we show that employing the 3D structure prior information yields accurate 3D scene layout segmentation.

A novel alternative method for 3D visualisation in Parasitology: the construction of a 3D model of a parasite from 2D illustrations.

Science.gov (United States)

Teo, B G; Sarinder, K K S; Lim, L H S

2010-08-01

Three-dimensional (3D) models of the marginal hooks, dorsal and ventral anchors, bars and haptoral reservoirs of a parasite, Sundatrema langkawiense Lim & Gibson, 2009 (Monogenea) were developed using the polygonal modelling method in Autodesk 3ds Max (Version 9) based on two-dimensional (2D) illustrations. Maxscripts were written to rotate the modelled 3D structures. Appropriately orientated 3D haptoral hard-parts were then selected and positioned within the transparent 3D outline of the haptor and grouped together to form a complete 3D haptoral entity. This technique is an inexpensive tool for constructing 3D models from 2D illustrations for 3D visualisation of the spatial relationships between the different structural parts within organisms.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Science.gov (United States)

Lewis, Tony E; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L; Buchan, Daniel W A; Chothia, Cyrus; Cuff, Alison; Dana, Jose M; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T; Kelley, Lawrence A; Kleywegt, Gerard J; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G; Ochoa-Montaño, Bernardo; Rackham, Owen J L; Smith, James; Sternberg, Michael J E; Velankar, Sameer; Yeats, Corin; Orengo, Christine

2013-01-01

Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence-structure-function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker's yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs).

Improving Semantic Updating Method on 3d City Models Using Hybrid Semantic-Geometric 3d Segmentation Technique

Science.gov (United States)

Sharkawi, K.-H.; Abdul-Rahman, A.

2013-09-01

Cities and urban areas entities such as building structures are becoming more complex as the modern human civilizations continue to evolve. The ability to plan and manage every territory especially the urban areas is very important to every government in the world. Planning and managing cities and urban areas based on printed maps and 2D data are getting insufficient and inefficient to cope with the complexity of the new developments in big cities. The emergence of 3D city models have boosted the efficiency in analysing and managing urban areas as the 3D data are proven to represent the real world object more accurately. It has since been adopted as the new trend in buildings and urban management and planning applications. Nowadays, many countries around the world have been generating virtual 3D representation of their major cities. The growing interest in improving the usability of 3D city models has resulted in the development of various tools for analysis based on the 3D city models. Today, 3D city models are generated for various purposes such as for tourism, location-based services, disaster management and urban planning. Meanwhile, modelling 3D objects are getting easier with the emergence of the user-friendly tools for 3D modelling available in the market. Generating 3D buildings with high accuracy also has become easier with the availability of airborne Lidar and terrestrial laser scanning equipments. The availability and accessibility to this technology makes it more sensible to analyse buildings in urban areas using 3D data as it accurately represent the real world objects. The Open Geospatial Consortium (OGC) has accepted CityGML specifications as one of the international standards for representing and exchanging spatial data, making it easier to visualize, store and manage 3D city models data efficiently. CityGML able to represents the semantics, geometry, topology and appearance of 3D city models in five well-defined Level-of-Details (LoD), namely LoD0

AxiSEM3D: broadband seismic wavefields in 3-D aspherical Earth models

Science.gov (United States)

Leng, K.; Nissen-Meyer, T.; Zad, K. H.; van Driel, M.; Al-Attar, D.

2017-12-01

Seismology is the primary tool for data-informed inference of Earth structure and dynamics. Simulating seismic wave propagation at a global scale is fundamental to seismology, but remains as one of most challenging problems in scientific computing, because of both the multiscale nature of Earth's interior and the observable frequency band of seismic data. We present a novel numerical method to simulate global seismic wave propagation in realistic 3-D Earth models. Our method, named AxiSEM3D, is a hybrid of spectral element method and pseudospectral method. It reduces the azimuthal dimension of wavefields by means of a global Fourier series parameterization, of which the number of terms can be locally adapted to the inherent azimuthal smoothness of the wavefields. AxiSEM3D allows not only for material heterogeneities, such as velocity, density, anisotropy and attenuation, but also for finite undulations on radial discontinuities, both solid-solid and solid-fluid, and thereby a variety of aspherical Earth features such as ellipticity, topography, variable crustal thickness, and core-mantle boundary topography. Such interface undulations are equivalently interpreted as material perturbations of the contiguous media, based on the "particle relabelling transformation". Efficiency comparisons show that AxiSEM3D can be 1 to 3 orders of magnitude faster than conventional 3-D methods, with the speedup increasing with simulation frequency and decreasing with model complexity, but for all realistic structures the speedup remains at least one order of magnitude. The observable frequency range of global seismic data (up to 1 Hz) has been covered for wavefield modelling upon a 3-D Earth model with reasonable computing resources. We show an application of surface wave modelling within a state-of-the-art global crustal model (Crust1.0), with the synthetics compared to real data. The high-performance C++ code is released at github.com/AxiSEM3D/AxiSEM3D.

3D Hilbert Space Filling Curves in 3D City Modeling for Faster Spatial Queries

DEFF Research Database (Denmark)

Ujang, Uznir; Antón Castro, Francesc/François; Azri, Suhaibah

2014-01-01

The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using...... method, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban...... objects. In this research, the authors propose an opponent data constellation technique of space-filling curves (3D Hilbert curves) for 3D city model data representation. Unlike previous methods, that try to project 3D or n-dimensional data down to 2D or 3D using Principal Component Analysis (PCA...

Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

Science.gov (United States)

Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

2016-01-01

Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

Structured Light-Based 3D Reconstruction System for Plants

OpenAIRE

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 regi...

RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality.

Science.gov (United States)

Borrel, Alexandre; Fourches, Denis

2017-12-01

There is a growing interest for the broad use of Augmented Reality (AR) and Virtual Reality (VR) in the fields of bioinformatics and cheminformatics to visualize complex biological and chemical structures. AR and VR technologies allow for stunning and immersive experiences, offering untapped opportunities for both research and education purposes. However, preparing 3D models ready to use for AR and VR is time-consuming and requires a technical expertise that severely limits the development of new contents of potential interest for structural biologists, medicinal chemists, molecular modellers and teachers. Herein we present the RealityConvert software tool and associated website, which allow users to easily convert molecular objects to high quality 3D models directly compatible for AR and VR applications. For chemical structures, in addition to the 3D model generation, RealityConvert also generates image trackers, useful to universally call and anchor that particular 3D model when used in AR applications. The ultimate goal of RealityConvert is to facilitate and boost the development and accessibility of AR and VR contents for bioinformatics and cheminformatics applications. http://www.realityconvert.com. dfourch@ncsu.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Determination and validation of mTOR kinase-domain 3D structure by homology modeling

Directory of Open Access Journals (Sweden)

Lakhlili W

2015-07-01

Full Text Available Wiame Lakhlili,1 Gwénaël Chevé,2 Abdelaziz Yasri,2 Azeddine Ibrahimi1 1Laboratoire de Biotechnologie (MedBiotech, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V de Rabat, Rabat, Morroco; 2OriBase Pharma, Cap Gamma, Parc Euromédecine, Montpellier, France Abstract: 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.Keywords: mTOR, homology modeling, mTOR kinase-domain, docking

Combining 3D structure of real video and synthetic objects

Science.gov (United States)

Kim, Man-Bae; Song, Mun-Sup; Kim, Do-Kyoon

1998-04-01

This paper presents a new approach of combining real video and synthetic objects. The purpose of this work is to use the proposed technology in the fields of advanced animation, virtual reality, games, and so forth. Computer graphics has been used in the fields previously mentioned. Recently, some applications have added real video to graphic scenes for the purpose of augmenting the realism that the computer graphics lacks in. This approach called augmented or mixed reality can produce more realistic environment that the entire use of computer graphics. Our approach differs from the virtual reality and augmented reality in the manner that computer- generated graphic objects are combined to 3D structure extracted from monocular image sequences. The extraction of the 3D structure requires the estimation of 3D depth followed by the construction of a height map. Graphic objects are then combined to the height map. The realization of our proposed approach is carried out in the following steps: (1) We derive 3D structure from test image sequences. The extraction of the 3D structure requires the estimation of depth and the construction of a height map. Due to the contents of the test sequence, the height map represents the 3D structure. (2) The height map is modeled by Delaunay triangulation or Bezier surface and each planar surface is texture-mapped. (3) Finally, graphic objects are combined to the height map. Because 3D structure of the height map is already known, Step (3) is easily manipulated. Following this procedure, we produced an animation video demonstrating the combination of the 3D structure and graphic models. Users can navigate the realistic 3D world whose associated image is rendered on the display monitor.

3D Modelling and Printing Technology to Produce Patient-Specific 3D Models.

Science.gov (United States)

Birbara, Nicolette S; Otton, James M; Pather, Nalini

2017-11-10

A comprehensive knowledge of mitral valve (MV) anatomy is crucial in the assessment of MV disease. While the use of three-dimensional (3D) modelling and printing in MV assessment has undergone early clinical evaluation, the precision and usefulness of this technology requires further investigation. This study aimed to assess and validate 3D modelling and printing technology to produce patient-specific 3D MV models. A prototype method for MV 3D modelling and printing was developed from computed tomography (CT) scans of a plastinated human heart. Mitral valve models were printed using four 3D printing methods and validated to assess precision. Cardiac CT and 3D echocardiography imaging data of four MV disease patients was used to produce patient-specific 3D printed models, and 40 cardiac health professionals (CHPs) were surveyed on the perceived value and potential uses of 3D models in a clinical setting. The prototype method demonstrated submillimetre precision for all four 3D printing methods used, and statistical analysis showed a significant difference (p3D printed models, particularly using multiple print materials, were considered useful by CHPs for preoperative planning, as well as other applications such as teaching and training. This study suggests that, with further advances in 3D modelling and printing technology, patient-specific 3D MV models could serve as a useful clinical tool. The findings also highlight the potential of this technology to be applied in a variety of medical areas within both clinical and educational settings. Copyright © 2017 Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) and the Cardiac Society of Australia and New Zealand (CSANZ). Published by Elsevier B.V. All rights reserved.

Direct ink writing of 3D conductive polyaniline structures and rheological modelling

Science.gov (United States)

Holness, F. Benjamin; Price, Aaron D.

2018-01-01

The intractable nature of conjugated polymers (CP) leads to practical limitations in the fabrication of CP-based transducers having complex three-dimensional geometries. Conventional CP device fabrication processes have focused primarily on thin-film deposition techniques; this study explores novel additive manufacturing processes specifically developed for CP with the ultimate goal of increasing the functionality of CP sensors and actuators. Herein we employ automated polymer paste extrusion processes for the direct ink writing of 3D conductive polyaniline (PANI) structures. Realization of these structures was enabled through a modified fused filament fabrication delta robot equipped with an integrated polymer paste extruder to fabricate high-resolution 3D conductive PANI structures. The required processability of PANI was achieved by means of a counterion-induced thermal doping method. The effect of thermal doping on the PANI-DBSA paste by means of a constitutive relationship to describe the paste flow as a function of the thermal doping time is explored. This relationship is incorporated within a flow model to predict the extruded track width as a function of various process parameters including: print speed, gauge pressure, nozzle diameter, and pre-extrusion thermal doping time.

Numerical modeling of 3D halo current path in ITER structures

Energy Technology Data Exchange (ETDEWEB)

Bettini, Paolo; Marconato, Nicolò; Furno Palumbo, Maurizio; Peruzzo, Simone [Consorzio RFX, EURATOM-ENEA Association, C.so Stati Uniti 4, 35127 Padova (Italy); Specogna, Ruben, E-mail: ruben.specogna@uniud.it [DIEGM, Università di Udine, Via delle Scienze, 208, 33100 Udine (Italy); Albanese, Raffaele; Rubinacci, Guglielmo; Ventre, Salvatore; Villone, Fabio [Consorzio CREATE, EURATOM-ENEA Association, Via Claudio 21, 80125 Napoli (Italy)

2013-10-15

Highlights: ► Two numerical codes for the evaluation of halo currents in 3D structures are presented. ► A simplified plasma model is adopted to provide the input (halo current injected into the FW). ► Two representative test cases of ITER symmetric and asymmetric VDEs have been analyzed. ► The proposed approaches provide results in excellent agreement for both cases. -- Abstract: Disruptions represent one of the main concerns for Tokamak operation, especially in view of fusion reactors, or experimental test reactors, due to the electro-mechanical loads induced by halo and eddy currents. The development of a predictive tool which allows to estimate the magnitude and spatial distribution of the halo current forces is of paramount importance in order to ensure robust vessel and in-vessel component design. With this aim, two numerical codes (CARIDDI, CAFE) have been developed, which allow to calculate the halo current path (resistive distribution) in the passive structures surrounding the plasma. The former is based on an integral formulation for the eddy currents problem particularized to the static case; the latter implements a pair of 3D FEM complementary formulations for the solution of the steady-state current conduction problem. A simplified plasma model is adopted to provide the inputs (halo current injected into the first wall). Two representative test cases (ITER symmetric and asymmetric VDEs) have been selected to cross check the results of the proposed approaches.

Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

Science.gov (United States)

Hossain, Md Anowar; Roslan, Hairul Azman

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.

3D MRI Modeling of Thin and Spatially Complex Soft Tissue Structures without Shrinkage: Lamprey Myosepta as an Example.

Science.gov (United States)

Wood, Bradley M; Jia, Guang; Carmichael, Owen; McKlveen, Kevin; Homberger, Dominique G

2018-05-12

3D imaging techniques enable the non-destructive analysis and modeling of complex structures. Among these, MRI exhibits good soft tissue contrast, but is currently less commonly used for non-clinical research than x-ray CT, even though the latter requires contrast-staining that shrinks and distorts soft tissues. When the objective is the creation of a realistic and complete 3D model of soft tissue structures, MRI data are more demanding to acquire and visualize and require extensive post-processing because they comprise non-cubic voxels with dimensions that represent a trade-off between tissue contrast and image resolution. Therefore, thin soft tissue structures with complex spatial configurations are not always visible in a single MRI dataset, so that standard segmentation techniques are not sufficient for their complete visualization. By using the example of the thin and spatially complex connective tissue myosepta in lampreys, we developed a workflow protocol for the selection of the appropriate parameters for the acquisition of MRI data and for the visualization and 3D modeling of soft tissue structures. This protocol includes a novel recursive segmentation technique for supplementing missing data in one dataset with data from another dataset to produce realistic and complete 3D models. Such 3D models are needed for the modeling of dynamic processes, such as the biomechanics of fish locomotion. However, our methodology is applicable to the visualization of any thin soft tissue structures with complex spatial configurations, such as fasciae, aponeuroses, and small blood vessels and nerves, for clinical research and the further exploration of tensegrity. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Modelling 3D spatial objects in a geo-DBMS using a 3D primitive

Science.gov (United States)

Arens, Călin; Stoter, Jantien; van Oosterom, Peter

2005-03-01

There is a growing interest in modelling the world in three dimensions, both in applications and in science. At the same time, geographical information systems are changing into integrated architecture in which administrative and spatial data are maintained in one environment. It is for this reason that mainstream Data Base Management Systems (DBMSs) have implemented spatial data types according to the 'Simple Feature Specifications for SQL', described by the OpenGeospatial Consortium. However, these specifications are 2D, as indeed are the implementations in DBMSs. At the Section GIS Technology of TU Delft, research has been carried out in which a 3D primitive was implemented in a DBMS (Oracle Spatial). To explore the possibilities and complications, a fairly simple 3D primitive was chosen to start with: a polyhedron. In the future the study will be extended with more complex primitives, the ultimate aim being to build 3D models with features closer to the real world. Besides the data structure, a validation function was developed to check the geometric accuracy of the data. Rules for validation were established and translated into prototype implementations with the aid of literature. In order to manipulate the data, a list of useful 3D functions was specified. Most of these were translated into algorithms, which were implemented in the DBMS. The algorithms for these functions were obtained from the relevant literature. The research also comprised a comparative performance test on spatial indexing in 2D and 3D, using an R-tree. Finally, existing software was used to visualize 3D objects structured with the implemented 3D primitive. This research is a first attempt to implement a true 3D primitive in a DBMS. Future research will focus on extending and improving the implementations and on optimizing maintenance and query of 3D objects in DBMSs.

Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

Directory of Open Access Journals (Sweden)

Md. Anowar Hossain

2014-01-01

Full Text Available 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/α8 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.

Creating physical 3D stereolithograph models of brain and skull.

Directory of Open Access Journals (Sweden)

Daniel J Kelley

2007-10-01

Full Text Available The human brain and skull are three dimensional (3D anatomical structures with complex surfaces. However, medical images are often two dimensional (2D and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50 used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine.

Fluid-structure interaction and structural analyses using a comprehensive mitral valve model with 3D chordal structure.

Science.gov (United States)

Toma, Milan; Einstein, Daniel R; Bloodworth, Charles H; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2017-04-01

Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be 'invisible' to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

3D visualisation of the middle ear and adjacent structures using reconstructed multi-slice CT datasets, correlating 3D images and virtual endoscopy to the 2D cross-sectional images

International Nuclear Information System (INIS)

Rodt, T.; Ratiu, P.; Kacher, D.F.; Anderson, M.; Jolesz, F.A.; Kikinis, R.; Becker, H.; Bartling, S.

2002-01-01

The 3D imaging of the middle ear facilitates better understanding of the patient's anatomy. Cross-sectional slices, however, often allow a more accurate evaluation of anatomical structures, as some detail may be lost through post-processing. In order to demonstrate the advantages of combining both approaches, we performed computed tomography (CT) imaging in two normal and 15 different pathological cases, and the 3D models were correlated to the cross-sectional CT slices. Reconstructed CT datasets were acquired by multi-slice CT. Post-processing was performed using the in-house software ''3D Slicer'', applying thresholding and manual segmentation. 3D models of the individual anatomical structures were generated and displayed in different colours. The display of relevant anatomical and pathological structures was evaluated in the greyscale 2D slices, 3D images, and the 2D slices showing the segmented 2D anatomy in different colours for each structure. Correlating 2D slices to the 3D models and virtual endoscopy helps to combine the advantages of each method. As generating 3D models can be extremely time-consuming, this approach can be a clinically applicable way of gaining a 3D understanding of the patient's anatomy by using models as a reference. Furthermore, it can help radiologists and otolaryngologists evaluating the 2D slices by adding the correct 3D information that would otherwise have to be mentally integrated. The method can be applied to radiological diagnosis, surgical planning, and especially, to teaching. (orig.)

Development of the Improving Process for the 3D Printed Structure

Science.gov (United States)

Takagishi, Kensuke; Umezu, Shinjiro

2017-01-01

The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

Development of the Improving Process for the 3D Printed Structure.

Science.gov (United States)

Takagishi, Kensuke; Umezu, Shinjiro

2017-01-05

The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics.

Modelling of MOCVD Reactor: New 3D Approach

Science.gov (United States)

Raj, E.; Lisik, Z.; Niedzielski, P.; Ruta, L.; Turczynski, M.; Wang, X.; Waag, A.

2014-04-01

The paper presents comparison of two different 3D models of vertical, rotating disc MOCVD reactor used for 3D GaN structure growth. The first one is based on the reactor symmetry, while the second, novel one incorporates only single line of showerhead nozzles. It is shown that both of them can be applied interchangeably regarding the phenomena taking place within the processing area. Moreover, the importance of boundary conditions regarding proper modelling of showerhead cooling and the significance of thermal radiation on temperature field within the modelled structure are presented and analysed. The last phenomenon is erroneously neglected in most of the hitherto studies.

Modelling of MOCVD reactor: new 3D approach

International Nuclear Information System (INIS)

Raj, E; Lisik, Z; Niedzielski, P; Ruta, L; Turczynski, M; Wang, X; Waag, A

2014-01-01

The paper presents comparison of two different 3D models of vertical, rotating disc MOCVD reactor used for 3D GaN structure growth. The first one is based on the reactor symmetry, while the second, novel one incorporates only single line of showerhead nozzles. It is shown that both of them can be applied interchangeably regarding the phenomena taking place within the processing area. Moreover, the importance of boundary conditions regarding proper modelling of showerhead cooling and the significance of thermal radiation on temperature field within the modelled structure are presented and analysed. The last phenomenon is erroneously neglected in most of the hitherto studies.

Improving 3D spatial queries search: newfangled technique of space filling curves in 3D city modeling

DEFF Research Database (Denmark)

Uznir, U.; Anton, François; Suhaibah, A.

2013-01-01

, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban objects......The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc.. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using...... modeling will improve data retrieval time by means of optimized 3D adjacency, nearest neighbor information and 3D indexing. The Hilbert mapping, which maps a subinterval of the [0, 1] interval to the corresponding portion of the d-dimensional Hilbert’s curve, preserves the Lebesgue measure and is Lipschitz...

Measuring Visual Closeness of 3-D Models

KAUST Repository

Gollaz Morales, Jose Alejandro

2012-09-01

Measuring visual closeness of 3-D models is an important issue for different problems and there is still no standardized metric or algorithm to do it. The normal of a surface plays a vital role in the shading of a 3-D object. Motivated by this, we developed two applications to measure visualcloseness, introducing normal difference as a parameter in a weighted metric in Metro’s sampling approach to obtain the maximum and mean distance between 3-D models using 3-D and 6-D correspondence search structures. A visual closeness metric should provide accurate information on what the human observers would perceive as visually close objects. We performed a validation study with a group of people to evaluate the correlation of our metrics with subjective perception. The results were positive since the metrics predicted the subjective rankings more accurately than the Hausdorff distance.

Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

Directory of Open Access Journals (Sweden)

Mihai V. Putz

2016-07-01

Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

MSX-3D: a tool to validate 3D protein models using mass spectrometry.

Science.gov (United States)

Heymann, Michaël; Paramelle, David; Subra, Gilles; Forest, Eric; Martinez, Jean; Geourjon, Christophe; Deléage, Gilbert

2008-12-01

The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking. We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment. Freely available at http://proteomics-pbil.ibcp.fr

A novel modeling method for manufacturing hearing aid using 3D medical images

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyeong Gyun [Dept of Radiological Science, Far East University, Eumseong (Korea, Republic of)

2016-06-15

This study aimed to suggest a novel method of modeling a hearing aid ear shell based on Digital Imaging and Communication in Medicine (DICOM) in the hearing aid ear shell manufacturing method using a 3D printer. In the experiment, a 3D external auditory meatus was extracted by using the critical values in the DICOM volume images, a nd t he modeling surface structures were compared in standard type STL (STereoLithography) files which could be recognized by a 3D printer. In this 3D modeling method, a conventional ear model was prepared, and the gaps between adjacent isograms produced by a 3D scanner were filled with 3D surface fragments to express the modeling structure. In this study, the same type of triangular surface structures were prepared by using the DICOM images. The result showed that the modeling surface structure based on the DICOM images provide the same environment that the conventional 3D printers may recognize, eventually enabling to print out the hearing aid ear shell shape.

A novel modeling method for manufacturing hearing aid using 3D medical images

International Nuclear Information System (INIS)

Kim, Hyeong Gyun

2016-01-01

This study aimed to suggest a novel method of modeling a hearing aid ear shell based on Digital Imaging and Communication in Medicine (DICOM) in the hearing aid ear shell manufacturing method using a 3D printer. In the experiment, a 3D external auditory meatus was extracted by using the critical values in the DICOM volume images, a nd t he modeling surface structures were compared in standard type STL (STereoLithography) files which could be recognized by a 3D printer. In this 3D modeling method, a conventional ear model was prepared, and the gaps between adjacent isograms produced by a 3D scanner were filled with 3D surface fragments to express the modeling structure. In this study, the same type of triangular surface structures were prepared by using the DICOM images. The result showed that the modeling surface structure based on the DICOM images provide the same environment that the conventional 3D printers may recognize, eventually enabling to print out the hearing aid ear shell shape

3dRPC: a web server for 3D RNA-protein structure prediction.

Science.gov (United States)

Huang, Yangyu; Li, Haotian; Xiao, Yi

2018-04-01

RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

NoSQL Based 3D City Model Management System

Science.gov (United States)

Mao, B.; Harrie, L.; Cao, J.; Wu, Z.; Shen, J.

2014-04-01

To manage increasingly complicated 3D city models, a framework based on NoSQL database is proposed in this paper. The framework supports import and export of 3D city model according to international standards such as CityGML, KML/COLLADA and X3D. We also suggest and implement 3D model analysis and visualization in the framework. For city model analysis, 3D geometry data and semantic information (such as name, height, area, price and so on) are stored and processed separately. We use a Map-Reduce method to deal with the 3D geometry data since it is more complex, while the semantic analysis is mainly based on database query operation. For visualization, a multiple 3D city representation structure CityTree is implemented within the framework to support dynamic LODs based on user viewpoint. Also, the proposed framework is easily extensible and supports geoindexes to speed up the querying. Our experimental results show that the proposed 3D city management system can efficiently fulfil the analysis and visualization requirements.

The lithospheric-scale 3D structural configuration of the North Alpine Foreland Basin constrained by gravity modelling and the calculation of the 3D load distribution

Science.gov (United States)

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

Modeling of 3D Aluminum Polycrystals during Large Deformations

International Nuclear Information System (INIS)

Maniatty, Antoinette M.; Littlewood, David J.; Lu Jing; Pyle, Devin

2007-01-01

An approach for generating, meshing, and modeling 3D polycrystals, with a focus on aluminum alloys, subjected to large deformation processes is presented. A Potts type model is used to generate statistically representative grain structures with periodicity to allow scale-linking. The grain structures are compared to experimentally observed grain structures to validate that they are representative. A procedure for generating a geometric model from the voxel data is developed allowing for adaptive meshing of the generated grain structure. Material behavior is governed by an appropriate crystal, elasto-viscoplastic constitutive model. The elastic-viscoplastic model is implemented in a three-dimensional, finite deformation, mixed, finite element program. In order to handle the large-scale problems of interest, a parallel implementation is utilized. A multiscale procedure is used to link larger scale models of deformation processes to the polycrystal model, where periodic boundary conditions on the fluctuation field are enforced. Finite-element models, of 3D polycrystal grain structures will be presented along with observations made from these simulations

Investigating the Importance of 3D Structure & Topography in Seismic Deformation Modeling: Case Study of the April 2015 Nepal Earthquake

Science.gov (United States)

Langer, L.; Gharti, H. N.; Tromp, J.

2017-12-01

In recent years, observations of deformation at plate boundaries have been greatly improved by the development of techniques in space geodesy. However, models of seismic deformation remain limited and are unable to account for realistic 3D structure in topography and material properties. We demonstrate the importance of 3D structure using a spectral-element method that incorporates fault geometry, topography, and heterogeneous material properties in a (non)linear viscoelastic domain. Our method is benchmarked against Okada's analytical technique and the PyLith software package. The April 2015 Nepal earthquake is used as a case study to examine whether 3D structure can affect the predictions of seismic deformation models. We find that the inclusion of topography has a significant effect on our results.

Using Openstreetmap Data to Generate Building Models with Their Inner Structures for 3d Maps

Science.gov (United States)

Wang, Z.; Zipf, A.

2017-09-01

With the development of Web 2.0, more and more data related to indoor environments has been collected within the volunteered geographic information (VGI) framework, which creates a need for construction of indoor environments from VGI. In this study, we focus on generating 3D building models from OpenStreetMap (OSM) data, and provide an approach to support construction and visualization of indoor environments on 3D maps. In this paper, we present an algorithm which can extract building information from OSM data, and can construct building structures as well as inner building components (e.g., doors, rooms, and windows). A web application is built to support the processing and visualization of the building models on a 3D map. We test our approach with an indoor dataset collected from the field. The results show the feasibility of our approach and its potentials to provide support for a wide range of applications, such as indoor and outdoor navigation, urban planning, and incident management.

USING OPENSTREETMAP DATA TO GENERATE BUILDING MODELS WITH THEIR INNER STRUCTURES FOR 3D MAPS

Directory of Open Access Journals (Sweden)

Z. Wang

2017-09-01

Full Text Available With the development of Web 2.0, more and more data related to indoor environments has been collected within the volunteered geographic information (VGI framework, which creates a need for construction of indoor environments from VGI. In this study, we focus on generating 3D building models from OpenStreetMap (OSM data, and provide an approach to support construction and visualization of indoor environments on 3D maps. In this paper, we present an algorithm which can extract building information from OSM data, and can construct building structures as well as inner building components (e.g., doors, rooms, and windows. A web application is built to support the processing and visualization of the building models on a 3D map. We test our approach with an indoor dataset collected from the field. The results show the feasibility of our approach and its potentials to provide support for a wide range of applications, such as indoor and outdoor navigation, urban planning, and incident management.

Evaluation of Fish Passage at Whitewater Parks Using 2D and 3D Hydraulic Modeling

Science.gov (United States)

Hardee, T.; Nelson, P. A.; Kondratieff, M.; Bledsoe, B. P.

2016-12-01

In-stream whitewater parks (WWPs) are increasingly popular recreational amenities that typically create waves by constricting flow through a chute to increase velocities and form a hydraulic jump. However, the hydraulic conditions these structures create can limit longitudinal habitat connectivity and potentially inhibit upstream fish migration, especially of native fishes. An improved understanding of the fundamental hydraulic processes and potential environmental effects of whitewater parks is needed to inform management decisions about Recreational In-Channel Diversions (RICDs). Here, we use hydraulic models to compute a continuous and spatially explicit description of velocity and depth along potential fish swimming paths in the flow field, and the ensemble of potential paths are compared to fish swimming performance data to predict fish passage via logistic regression analysis. While 3d models have been shown to accurately predict trout movement through WWP structures, 2d methods can provide a more cost-effective and manager-friendly approach to assessing the effects of similar hydraulic structures on fish passage when 3d analysis in not feasible. Here, we use 2d models to examine the hydraulics in several WWP structures on the North Fork of the St. Vrain River at Lyons, Colorado, and we compare these model results to fish passage predictions from a 3d model. Our analysis establishes a foundation for a practical, transferable and physically-rigorous 2d modeling approach for mechanistically evaluating the effects of hydraulic structures on fish passage.

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

Energy Technology Data Exchange (ETDEWEB)

Nugraha, Andri Dian [Global Geophysics Research Group, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia); Syahputra, Ahmad [Geophyisical Engineering, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia); Fatkhan,; Sule, Rachmat [Applied Geophysics Research Group, Faculty of Mining and Petroleum Engineering, Institute of Technology Bandung, Jalan Ganesha No. 10 Bandung, 40132 (Indonesia)

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.

Development of the Improving Process for the 3D Printed Structure

OpenAIRE

Kensuke Takagishi; Shinjiro Umezu

2017-01-01

The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able...

Computerized modeling techniques predict the 3D structure of H₄R: facts and fiction.

Science.gov (United States)

Zaid, Hilal; Ismael-Shanak, Siba; Michaeli, Amit; Rayan, Anwar

2012-01-01

The functional characterization of proteins presents a daily challenge r biochemical, medical and computational sciences, especially when the structures are undetermined empirically, as in the case of the Histamine H4 Receptor (H₄R). H₄R is a member of the GPCR superfamily that plays a vital role in immune and inflammatory responses. To date, the concept of GPCRs modeling is highlighted in textbooks and pharmaceutical pamphlets, and this group of proteins has been the subject of almost 3500 publications in the scientific literature. The dynamic nature of determining the GPCRs structure was elucidated through elegant and creative modeling methodologies, implemented by many groups around the world. H₄R which belongs to the GPCR family was cloned in 2000; understandably, its biological activity was reported only 65 times in pubmed. Here we attempt to cover the fundamental concepts of H₄R structure modeling and its implementation in drug discovery, especially those that have been experimentally tested and to highlight some ideas that are currently being discussed on the dynamic nature of H₄R and GPCRs computerized techniques for 3D structure modeling.

3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

Science.gov (United States)

Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

2009-06-01

Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

An asymptotic homogenization model for smart 3D grid-reinforced composite structures with generally orthotropic constituents

International Nuclear Information System (INIS)

Hassan, E M; Kalamkarov, A L; Georgiades, A V; Challagulla, K S

2009-01-01

A comprehensive micromechanical model for smart 3D composite structures reinforced with a periodic grid of generally orthotropic cylindrical reinforcements that also exhibit piezoelectric behavior is developed. The original boundary value problem characterizing the piezothermoelastic behavior of these structures is decoupled into a set of three simpler unit cell problems dealing, separately, with the elastic, piezoelectric and thermal expansion characteristics of the smart composite. The technique used is that of asymptotic homogenization and the solution of the unit cell problems permits determination of the effective elastic, piezoelectric and thermal expansion coefficients. The general orthotropy of the constituent materials is very important from the practical viewpoint and makes the analysis much more complicated. Several examples of practical interest are used to illustrate the work including smart 3D composites with cubic and conical embedded grids as well as diagonally reinforced smart structures. It is also shown in this work that in the limiting particular case of 2D grid-reinforced structures with isotropic reinforcements our results converge to earlier published results

Combining 3d Volume and Mesh Models for Representing Complicated Heritage Buildings

Science.gov (United States)

Tsai, F.; Chang, H.; Lin, Y.-W.

2017-08-01

This study developed a simple but effective strategy to combine 3D volume and mesh models for representing complicated heritage buildings and structures. The idea is to seamlessly integrate 3D parametric or polyhedral models and mesh-based digital surfaces to generate a hybrid 3D model that can take advantages of both modeling methods. The proposed hybrid model generation framework is separated into three phases. Firstly, after acquiring or generating 3D point clouds of the target, these 3D points are partitioned into different groups. Secondly, a parametric or polyhedral model of each group is generated based on plane and surface fitting algorithms to represent the basic structure of that region. A "bare-bones" model of the target can subsequently be constructed by connecting all 3D volume element models. In the third phase, the constructed bare-bones model is used as a mask to remove points enclosed by the bare-bones model from the original point clouds. The remaining points are then connected to form 3D surface mesh patches. The boundary points of each surface patch are identified and these boundary points are projected onto the surfaces of the bare-bones model. Finally, new meshes are created to connect the projected points and original mesh boundaries to integrate the mesh surfaces with the 3D volume model. The proposed method was applied to an open-source point cloud data set and point clouds of a local historical structure. Preliminary results indicated that the reconstructed hybrid models using the proposed method can retain both fundamental 3D volume characteristics and accurate geometric appearance with fine details. The reconstructed hybrid models can also be used to represent targets in different levels of detail according to user and system requirements in different applications.

Improving 3d Spatial Queries Search: Newfangled Technique of Space Filling Curves in 3d City Modeling

Science.gov (United States)

Uznir, U.; Anton, F.; Suhaibah, A.; Rahman, A. A.; Mioc, D.

2013-09-01

The advantages of three dimensional (3D) city models can be seen in various applications including photogrammetry, urban and regional planning, computer games, etc.. They expand the visualization and analysis capabilities of Geographic Information Systems on cities, and they can be developed using web standards. However, these 3D city models consume much more storage compared to two dimensional (2D) spatial data. They involve extra geometrical and topological information together with semantic data. Without a proper spatial data clustering method and its corresponding spatial data access method, retrieving portions of and especially searching these 3D city models, will not be done optimally. Even though current developments are based on an open data model allotted by the Open Geospatial Consortium (OGC) called CityGML, its XML-based structure makes it challenging to cluster the 3D urban objects. In this research, we propose an opponent data constellation technique of space-filling curves (3D Hilbert curves) for 3D city model data representation. Unlike previous methods, that try to project 3D or n-dimensional data down to 2D or 3D using Principal Component Analysis (PCA) or Hilbert mappings, in this research, we extend the Hilbert space-filling curve to one higher dimension for 3D city model data implementations. The query performance was tested using a CityGML dataset of 1,000 building blocks and the results are presented in this paper. The advantages of implementing space-filling curves in 3D city modeling will improve data retrieval time by means of optimized 3D adjacency, nearest neighbor information and 3D indexing. The Hilbert mapping, which maps a subinterval of the [0, 1] interval to the corresponding portion of the d-dimensional Hilbert's curve, preserves the Lebesgue measure and is Lipschitz continuous. Depending on the applications, several alternatives are possible in order to cluster spatial data together in the third dimension compared to its

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

Science.gov (United States)

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

Microfabricating 3D Structures by Laser Origami

Science.gov (United States)

2011-11-09

10.1117/2.1201111.003952 Microfabricating 3D structures by laser origami Alberto Piqué, Scott Mathews, Andrew Birnbaum, and Nicholas Charipar A new...folding known as origami allows the transformation of flat patterns into 3D shapes. A similar approach can be used to generate 3D structures com... geometries . The overarching challenge is to move away from traditional planar semiconductor photolitho- graphic techniques, which severely limit the type of

Structured Light-Based 3D Reconstruction System for Plants

Directory of Open Access Journals (Sweden)

Thuy Tuong Nguyen

2015-07-01

Full Text Available 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.

Structured Light-Based 3D Reconstruction System for Plants.

Science.gov (United States)

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

2015-07-29

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.

Mechanical Modelling of Pultrusion Process: 2D and 3D Numerical Approaches

DEFF Research Database (Denmark)

Baran, Ismet; Hattel, Jesper Henri; Akkerman, Remko

2015-01-01

The process induced variations such as residual stresses and distortions are a critical issue in pultrusion, since they affect the structural behavior as well as the mechanical properties and geometrical precision of the final product. In order to capture and investigate these variations......, a mechanical analysis should be performed. In the present work, the two dimensional (2D) quasi-static plane strain mechanical model for the pultrusion of a thick square profile developed by the authors is further improved using generalized plane strain elements. In addition to that, a more advanced 3D thermo......-chemical-mechanical analysis is carried out using 3D quadratic elements which is a novel application for the numerical modelling of the pultrusion process. It is found that the 2D mechanical models give relatively reasonable and accurate stress and displacement evolutions in the transverse direction as compared to the 3D...

Novel Low Cost 3D Surface Model Reconstruction System for Plant Phenotyping

Directory of Open Access Journals (Sweden)

Suxing Liu

2017-09-01

Full Text Available Accurate high-resolution three-dimensional (3D models are essential for a non-invasive analysis of phenotypic characteristics of plants. Previous limitations in 3D computer vision algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present an image-based 3D plant reconstruction system that can be achieved by using a single camera and a rotation stand. Our method is based on the structure from motion method, with a SIFT image feature descriptor. In order to improve the quality of the 3D models, we segmented the plant objects based on the PlantCV platform. We also deducted the optimal number of images needed for reconstructing a high-quality model. Experiments showed that an accurate 3D model of the plant was successfully could be reconstructed by our approach. This 3D surface model reconstruction system provides a simple and accurate computational platform for non-destructive, plant phenotyping.

3D Digital Modelling

DEFF Research Database (Denmark)

Hundebøl, Jesper

wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3...... important to appreciate the analysis. Before turning to the presentation of preliminary findings and a discussion of 3D digital modelling, it begins, however, with an outline of industry specific ICT strategic issues. Paper type. Multi-site field study...

GENERATING ACCURATE 3D MODELS OF ARCHITECTURAL HERITAGE STRUCTURES USING LOW-COST CAMERA AND OPEN SOURCE ALGORITHMS

Directory of Open Access Journals (Sweden)

M. Zacharek

2017-05-01

Full Text Available These studies have been conductedusing non-metric digital camera and dense image matching algorithms, as non-contact methods of creating monuments documentation.In order toprocess the imagery, few open-source software and algorithms of generating adense point cloud from images have been executed. In the research, the OSM Bundler, VisualSFM software, and web application ARC3D were used. Images obtained for each of the investigated objects were processed using those applications, and then dense point clouds and textured 3D models were created. As a result of post-processing, obtained models were filtered and scaled.The research showedthat even using the open-source software it is possible toobtain accurate 3D models of structures (with an accuracy of a few centimeters, but for the purpose of documentation and conservation of cultural and historical heritage, such accuracy can be insufficient.

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

Science.gov (United States)

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

2018-01-01

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

Methods and uncertainty estimations of 3-D structural modelling in crystalline rocks: a case study

Science.gov (United States)

Schneeberger, Raphael; de La Varga, Miguel; Egli, Daniel; Berger, Alfons; Kober, Florian; Wellmann, Florian; Herwegh, Marco

2017-09-01

Exhumed basement rocks are often dissected by faults, the latter controlling physical parameters such as rock strength, porosity, or permeability. Knowledge on the three-dimensional (3-D) geometry of the fault pattern and its continuation with depth is therefore of paramount importance for applied geology projects (e.g. tunnelling, nuclear waste disposal) in crystalline bedrock. The central Aar massif (Central Switzerland) serves as a study area where we investigate the 3-D geometry of the Alpine fault pattern by means of both surface (fieldwork and remote sensing) and underground ground (mapping of the Grimsel Test Site) information. The fault zone pattern consists of planar steep major faults (kilometre scale) interconnected with secondary relay faults (hectometre scale). Starting with surface data, we present a workflow for structural 3-D modelling of the primary faults based on a comparison of three extrapolation approaches based on (a) field data, (b) Delaunay triangulation, and (c) a best-fitting moment of inertia analysis. The quality of these surface-data-based 3-D models is then tested with respect to the fit of the predictions with the underground appearance of faults. All three extrapolation approaches result in a close fit ( > 10 %) when compared with underground rock laboratory mapping. Subsequently, we performed a statistical interpolation based on Bayesian inference in order to validate and further constrain the uncertainty of the extrapolation approaches. This comparison indicates that fieldwork at the surface is key for accurately constraining the geometry of the fault pattern and enabling a proper extrapolation of major faults towards depth. Considerable uncertainties, however, persist with respect to smaller-sized secondary structures because of their limited spatial extensions and unknown reoccurrence intervals.

Integrated Biogeomorphological Modeling Using Delft3D

Science.gov (United States)

Ye, Q.; Jagers, B.

2011-12-01

The skill of numerical morphological models has improved significantly from the early 2D uniform, total load sediment models (with steady state or infrequent wave updates) to recent 3D hydrodynamic models with multiple suspended and bed load sediment fractions and bed stratigraphy (online coupled with waves). Although there remain many open questions within this combined field of hydro- and morphodynamics, we observe an increasing need to include biological processes in the overall dynamics. In riverine and inter-tidal environments, there is often an important influence by riparian vegetation and macrobenthos. Over the past decade more and more researchers have started to extend the simulation environment with wrapper scripts and other quick code hacks to estimate their influence on morphological development in coastal, estuarine and riverine environments. Although one can in this way quickly analyze different approaches, these research tools have generally not been designed with reuse, performance and portability in mind. We have now implemented a reusable, flexible, and efficient two-way link between the Delft3D open source framework for hydrodynamics, waves and morphology, and the water quality and ecology modules. The same link will be used for 1D, 2D and 3D modeling on networks and both structured and unstructured grids. We will describe the concepts of the overall system, and illustrate it with some first results.

3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups

Science.gov (United States)

Scalfani, Vincent F.; Vaid, Thomas P.

2014-01-01

Tangible models help students and researchers visualize chemical structures in three dimensions (3D). 3D printing offers a unique and straightforward approach to fabricate plastic 3D models of molecules and extended solids. In this article, we prepared a series of digital 3D design files of molecular structures that will be useful for teaching…

Vascular stents: Coupling full 3-D with reduced-order structural models

International Nuclear Information System (INIS)

Avdeev, I; Shams, M

2010-01-01

Self-expanding nitinol stents are used to treat peripheral arterial disease. The peripheral arteries are subjected to a combination of mechanical forces such as compression, torsion, bending, and contraction. Most commercially available peripheral self-expanding stents are composed of a series of sub-millimeter V-shaped struts, which are laser-cut from a nitinol tube and surface-treated for better fatigue performance. The numerical stent models must accurately predict location and distribution of local stresses and strains caused by large arterial deformations. Full 3-D finite element non-linear analysis of an entire stent is computationally expensive to the point of being prohibitive, especially for longer stents. Reduced-order models based on beam or shell elements are fairly accurate in capturing global deformations, but are not very helpful in predicting stent failure. We propose a mixed approach that combines the full 3-D model and reduced-order models. Several global-local, full 3-D/reduced-order finite element models of a peripheral self-expanding stent were validated and compared with experimental data. The kinematic constraint method used to couple various elements together was found to be very efficient and easily applicable to commercial FEA codes. The proposed mixed models can be used to accurately predict stent failure based on realistic (patient-specific), non-linear kinematic behavior of peripheral arteries.

Combined shape and topology optimization of 3D structures

DEFF Research Database (Denmark)

Christiansen, Asger Nyman; Bærentzen, Jakob Andreas; Nobel-Jørgensen, Morten

2015-01-01

We present a method for automatic generation of 3D models based on shape and topology optimization. The optimization procedure, or model generation process, is initialized by a set of boundary conditions, an objective function, constraints and an initial structure. Using this input, the method...... will automatically deform and change the topology of the initial structure such that the objective function is optimized subject to the specified constraints and boundary conditions. For example, this tool can be used to improve the stiffness of a structure before printing, reduce the amount of material needed...

Shape: A 3D Modeling Tool for Astrophysics.

Science.gov (United States)

Steffen, Wolfgang; Koning, Nicholas; Wenger, Stephan; Morisset, Christophe; Magnor, Marcus

2011-04-01

We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type, and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.

3D Product authenticity model for online retail: An invariance analysis

Directory of Open Access Journals (Sweden)

Algharabat, R.

2010-01-01

Full Text Available This study investigates the effects of different levels of invariance analysis on three dimensional (3D product authenticity model (3DPAM constructs in the e- retailing context. A hypothetical retailer website presents a variety of laptops using 3D product visualisations. The proposed conceptual model achieves acceptable fit and the hypothesised paths are all valid. We empirically investigate the invariance across the subgroups to validate the results of our 3DPAM. We concluded that the 3D product authenticity model construct was invariant for our sample across different gender, level of education and study backgrounds. These findings suggested that all our subgroups conceptualised the 3DPAM similarly. Also the results show some non-invariance results for the structural and latent mean models. The gender group posits a non-invariance latent mean model. Study backgrounds group reveals a non-invariance result for the structural model. These findings allowed us to understand the 3DPAMs validity in the e-retail context. Managerial implications are explained.

QUIESCENT PROMINENCES IN THE ERA OF ALMA: SIMULATED OBSERVATIONS USING THE 3D WHOLE-PROMINENCE FINE STRUCTURE MODEL

Energy Technology Data Exchange (ETDEWEB)

Gunár, Stanislav; Heinzel, Petr [Astronomical Institute, The Czech Academy of Sciences, 25165 Ondřejov (Czech Republic); Mackay, Duncan H. [School of Mathematics and Statistics, University of St Andrews, North Haugh, St Andrews KY16 9SS (United Kingdom); Anzer, Ulrich [Max-Planck-Institut für Astrophysik, Karl-Schwarzschild-Str. 1, D-85740 Garching bei München (Germany)

2016-12-20

We use the detailed 3D whole-prominence fine structure model to produce the first simulated high-resolution ALMA observations of a modeled quiescent solar prominence. The maps of synthetic brightness temperature and optical thickness shown in the present paper are produced using a visualization method for synthesis of the submillimeter/millimeter radio continua. We have obtained the simulated observations of both the prominence at the limb and the filament on the disk at wavelengths covering a broad range that encompasses the full potential of ALMA. We demonstrate here extent to which the small-scale and large-scale prominence and filament structures will be visible in the ALMA observations spanning both the optically thin and thick regimes. We analyze the relationship between the brightness and kinetic temperature of the prominence plasma. We also illustrate the opportunities ALMA will provide for studying the thermal structure of the prominence plasma from the cores of the cool prominence fine structure to the prominence–corona transition region. In addition, we show that detailed 3D modeling of entire prominences with their numerous fine structures will be important for the correct interpretation of future ALMA observations of prominences.

Modeling 3-D solar wind structure

Czech Academy of Sciences Publication Activity Database

Odstrčil, Dušan

2003-01-01

Roč. 32, č. 4 (2003), s. 497-506 ISSN 0273-1177 R&D Projects: GA AV ČR IAA3003003; GA AV ČR IBS1003006 Institutional research plan: CEZ:AV0Z1003909 Keywords : solar wind * modeling Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 0.483, year: 2003

Fine reservoir structure modeling based upon 3D visualized stratigraphic correlation between horizontal wells: methodology and its application

Science.gov (United States)

Chenghua, Ou; Chaochun, Li; Siyuan, Huang; Sheng, James J.; Yuan, Xu

2017-12-01

As the platform-based horizontal well production mode has been widely applied in petroleum industry, building a reliable fine reservoir structure model by using horizontal well stratigraphic correlation has become very important. Horizontal wells usually extend between the upper and bottom boundaries of the target formation, with limited penetration points. Using these limited penetration points to conduct well deviation correction means the formation depth information obtained is not accurate, which makes it hard to build a fine structure model. In order to solve this problem, a method of fine reservoir structure modeling, based on 3D visualized stratigraphic correlation among horizontal wells, is proposed. This method can increase the accuracy when estimating the depth of the penetration points, and can also effectively predict the top and bottom interfaces in the horizontal penetrating section. Moreover, this method will greatly increase not only the number of points of depth data available, but also the accuracy of these data, which achieves the goal of building a reliable fine reservoir structure model by using the stratigraphic correlation among horizontal wells. Using this method, four 3D fine structure layer models have been successfully built of a specimen shale gas field with platform-based horizontal well production mode. The shale gas field is located to the east of Sichuan Basin, China; the successful application of the method has proven its feasibility and reliability.

Precision structural engineering of self-rolled-up 3D nanomembranes guided by transient quasi-static FEM modeling.

Science.gov (United States)

Huang, Wen; Koric, Seid; Yu, Xin; Hsia, K Jimmy; Li, Xiuling

2014-11-12

Micro- and nanoscale tubular structures can be formed by strain-induced self-rolled-up nanomembranes. Precision engineering of the shape and dimension determines the performance of devices based on this platform for electronic, optical, and biological applications. A transient quasi-static finite element method (FEM) with moving boundary conditions is proposed as a general approach to design diverse types of three-dimensional (3D) rolled-up geometries. This method captures the dynamic release process of membranes through etching driven by mismatch strain and accurately predicts the final dimensions of rolled-up structures. Guided by the FEM modeling, experimental demonstration using silicon nitride membranes was achieved with unprecedented precision including controlling fractional turns of a rolled-up membrane, anisotropic rolling to form helical structures, and local stress control for 3D hierarchical architectures.

Methods and uncertainty estimations of 3-D structural modelling in crystalline rocks: a case study

Directory of Open Access Journals (Sweden)

R. Schneeberger

2017-09-01

Full Text Available Exhumed basement rocks are often dissected by faults, the latter controlling physical parameters such as rock strength, porosity, or permeability. Knowledge on the three-dimensional (3-D geometry of the fault pattern and its continuation with depth is therefore of paramount importance for applied geology projects (e.g. tunnelling, nuclear waste disposal in crystalline bedrock. The central Aar massif (Central Switzerland serves as a study area where we investigate the 3-D geometry of the Alpine fault pattern by means of both surface (fieldwork and remote sensing and underground ground (mapping of the Grimsel Test Site information. The fault zone pattern consists of planar steep major faults (kilometre scale interconnected with secondary relay faults (hectometre scale. Starting with surface data, we present a workflow for structural 3-D modelling of the primary faults based on a comparison of three extrapolation approaches based on (a field data, (b Delaunay triangulation, and (c a best-fitting moment of inertia analysis. The quality of these surface-data-based 3-D models is then tested with respect to the fit of the predictions with the underground appearance of faults. All three extrapolation approaches result in a close fit (> 10 % when compared with underground rock laboratory mapping. Subsequently, we performed a statistical interpolation based on Bayesian inference in order to validate and further constrain the uncertainty of the extrapolation approaches. This comparison indicates that fieldwork at the surface is key for accurately constraining the geometry of the fault pattern and enabling a proper extrapolation of major faults towards depth. Considerable uncertainties, however, persist with respect to smaller-sized secondary structures because of their limited spatial extensions and unknown reoccurrence intervals.

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.

Science.gov (United States)

Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

2010-07-01

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

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

Science.gov (United States)

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

3D Model Optimization of Four-Facet Drill for 3D Drilling Simulation

Directory of Open Access Journals (Sweden)

Buranský Ivan

2016-09-01

Full Text Available The article is focused on optimization of four-facet drill for 3D drilling numerical modelling. For optimization, the process of reverse engineering by PowerShape software was used. The design of four-facet drill was created in NumrotoPlus software. The modified 3D model of the drill was used in the numerical analysis of cutting forces. Verification of the accuracy of 3D models for reverse engineering was implemented using the colour deviation maps. The CAD model was in the STEP format. For simulation software, 3D model in the STEP format is ideal. STEP is a solid model. Simulation software automatically splits the 3D model into finite elements. The STEP model was therefore more suitable than the STL model.

AxiSEM3D: a new fast method for global wave propagation in 3-D Earth models with undulating discontinuities

Science.gov (United States)

Leng, K.; Nissen-Meyer, T.; van Driel, M.; Al-Attar, D.

2016-12-01

We present a new, computationally efficient numerical method to simulate global seismic wave propagation in realistic 3-D Earth models with laterally heterogeneous media and finite boundary perturbations. Our method is a hybrid of pseudo-spectral and spectral element methods (SEM). We characterize the azimuthal dependence of 3-D wavefields in terms of Fourier series, such that the 3-D equations of motion reduce to an algebraic system of coupled 2-D meridional equations, which can be solved by a 2-D spectral element method (based on www.axisem.info). Computational efficiency of our method stems from lateral smoothness of global Earth models (with respect to wavelength) as well as axial singularity of seismic point sources, which jointly confine the Fourier modes of wavefields to a few lower orders. All boundary perturbations that violate geometric spherical symmetry, including Earth's ellipticity, topography and bathymetry, undulations of internal discontinuities such as Moho and CMB, are uniformly considered by means of a Particle Relabeling Transformation.The MPI-based high performance C++ code AxiSEM3D, is now available for forward simulations upon 3-D Earth models with fluid outer core, ellipticity, and both mantle and crustal structures. We show novel benchmarks for global wave solutions in 3-D mantle structures between our method and an independent, fully discretized 3-D SEM with remarkable agreement. Performance comparisons are carried out on three state-of-the-art tomography models, with seismic period going down to 5s. It is shown that our method runs up to two orders of magnitude faster than the 3-D SEM for such settings, and such computational advantage scales favourably with seismic frequency. By examining wavefields passing through hypothetical Gaussian plumes of varying sharpness, we identify in model-wavelength space the limits where our method may lose its advantage.

Combretastatin A-4 based thiophene derivatives as antitumor agent: Development of structure activity correlation model using 3D-QSAR, pharmacophore and docking studies

Directory of Open Access Journals (Sweden)

Vijay K. Patel

2017-12-01

Full Text Available The structure and ligand based synergistic approach is being applied to design ligands more correctly. The present report discloses the combination of structure and ligand based tactics i.e., molecular docking, energetic based pharmacophore, pharmacophore and atom based 3D-QSAR modeling for the analysis of thiophene derivatives as anticancer agent. The main purpose of using structure and ligand based synergistic approach is to ascertain a correlation between structure and its biological activity. Thiophene derivatives have been found to possess cytotoxic activity in several cancer cell lines and its mechanism of action basically involves the binding to the colchicine site on β-tubulin. The structure based approach (molecular docking was performed on a series of thiophene derivatives. All the structures were docked to colchicine binding site of β tubulin for examining the binding affinity of compounds for antitumor activity. The pharmacophore and atom based 3D-QSAR modeling was accomplished on a series of thiophene (32 compounds analogues. Five-point common pharmacophore hypotheses (AAAAR.38 were selected for alignment of all compounds. The atom based 3D-QSAR models were developed by selection of 23 compounds as training set and 9 compounds as test set, demonstrated good partial least squares statistical results. The generated common pharmacophore hypothesis and 3D-QSAR models were validated further externally by measuring the activity of database compounds and assessing it with actual activity. The common pharmacophore hypothesis AAAAR.38 resulted in a 3D-QSAR model with excellent PLSs data for factor two characterized by the best predication coefficient Q2 (cross validated r2 (0.7213, regression R2 (0.8311, SD (0.3672, F (49.2, P (1.89E-08, RMSE (0.3864, Stability (0.8702, Pearson-r (0.8722. The results of these molecular modeling studies i.e., molecular docking, energetic based pharmacophore, pharmacophore and atom based 3D-QSAR modeling

Modeling and Reconstruction of Micro-structured 3D Chitosan/Gelatin Porous Scaffolds Using Micro-CT

Science.gov (United States)

Gong, Haibo; Li, Dichen; He, Jiankang; Liu, Yaxiong; Lian, Qin; Zhao, Jinna

2008-09-01

Three dimensional (3D) channel networks are the key to promise the uniform distribution of nutrients inside 3D hepatic tissue engineering scaffolds and prompt elimination of metabolic products out of the scaffolds. 3D chitosan/gelatin porous scaffolds with predefined internal channels were fabricated and a combination of light microscope, laser confocal microscopy and micro-CT were employed to characterize the structure of porous scaffolds. In order to evaluate the flow field distribution inside the micro-structured 3D scaffolds, a computer reconstructing method based on Micro-CT was proposed. According to this evaluating method, a contrast between 3D porous scaffolds with and without predefined internal channels was also performed to assess scaffolds' fluid characters. Results showed that the internal channel of the 3D scaffolds formed the 3D fluid channel network; the uniformity of flow field distribution of the scaffolds fabricated in this paper was better than the simple porous scaffold without micro-fluid channels.

3D Geothermal Modelling of the Mount Amiata Hydrothermal System in Italy

Directory of Open Access Journals (Sweden)

Paolo Fulignati

2014-11-01

Full Text Available In this paper we build a subsurface model that helps in visualizing and understanding the structural framework, geology and their interactions with the Mt. Amiata geothermal system. Modelling in 3D provides the possibility to interpolate the geometry of structures and is an effective way of understanding geological features. The 3D modelling approach appears to be crucial for further progress in the reconstruction of the assessment of the geothermal model of Mt. Amiata. Furthermore, this model is used as the basis of a 3D numerical thermo-fluid-dynamic model of the existing reservoir(s. The integration between borehole data and numerical modelling results allows reconstructing the temperature distribution in the subsoil of the Mt. Amiata area.

3D high-resolution two-photon crosslinked hydrogel structures for biological studies.

Science.gov (United States)

Brigo, Laura; Urciuolo, Anna; Giulitti, Stefano; Della Giustina, Gioia; Tromayer, Maximilian; Liska, Robert; Elvassore, Nicola; Brusatin, Giovanna

2017-06-01

Hydrogels are widely used as matrices for cell growth due to the their tuneable chemical and physical properties, which mimic the extracellular matrix of natural tissue. The microfabrication of hydrogels into arbitrarily complex 3D structures is becoming essential for numerous biological applications, and in particular for investigating the correlation between cell shape and cell function in a 3D environment. Micrometric and sub-micrometric resolution hydrogel scaffolds are required to deeply investigate molecular mechanisms behind cell-matrix interaction and downstream cellular processes. We report the design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking. Hydrated structures of lateral linewidth down to 0.5µm, lateral and axial resolution down to a few µm are demonstrated. According to the processing parameters, different degrees of polymerization are obtained, resulting in hydrated scaffolds of variable swelling and deformation. The 3D hydrogels are biocompatible and promote cell adhesion and migration. Interestingly, according to the polymerization degree, 3D hydrogel woodpile structures show variable extent of cell adhesion and invasion. Human BJ cell lines show capability of deforming 3D micrometric resolved hydrogel structures. The design and development of high resolution 3D gelatin hydrogel woodpile structures by two-photon crosslinking is reported. Significantly, topological and mechanical conditions of polymerized gelatin structures were suitable for cell accommodation in the volume of the woodpiles, leading to a cell density per unit area comparable to the bare substrate. The fabricated structures, presenting micrometric features of high resolution, are actively deformed by cells, both in terms of cell invasion within rods and of cell attachment in-between contiguous woodpiles. Possible biological targets for this 3D approach are customized 3D tissue models, or studies of cell adhesion

Method for modeling post-mortem biometric 3D fingerprints

Science.gov (United States)

Rajeev, Srijith; Shreyas, Kamath K. M.; Agaian, Sos S.

2016-05-01

Despite the advancements of fingerprint recognition in 2-D and 3-D domain, authenticating deformed/post-mortem fingerprints continue to be an important challenge. Prior cleansing and reconditioning of the deceased finger is required before acquisition of the fingerprint. The victim's finger needs to be precisely and carefully operated by a medium to record the fingerprint impression. This process may damage the structure of the finger, which subsequently leads to higher false rejection rates. This paper proposes a non-invasive method to perform 3-D deformed/post-mortem finger modeling, which produces a 2-D rolled equivalent fingerprint for automated verification. The presented novel modeling method involves masking, filtering, and unrolling. Computer simulations were conducted on finger models with different depth variations obtained from Flashscan3D LLC. Results illustrate that the modeling scheme provides a viable 2-D fingerprint of deformed models for automated verification. The quality and adaptability of the obtained unrolled 2-D fingerprints were analyzed using NIST fingerprint software. Eventually, the presented method could be extended to other biometric traits such as palm, foot, tongue etc. for security and administrative applications.

Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors

DEFF Research Database (Denmark)

Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

2016-01-01

study, we used the structure prediction tools PIGS and I-TASSER for creating the 3D models and the TM-align algorithm to superpose them. The innovation of the current methodology resides in the usage of methods adapted from 3D content-based search methodologies to determine the local structural...... determine it are extremely laborious and demanding. Hence, the ability to gain insight into the structure of Igs at large relies on the availability of tools and algorithms for producing accurate Ig structural models based on their primary sequence alone. These models can then be used to determine...... to achieve an optimal solution to this task yet their results were hindered mainly due to the lack of efficient clustering methods based on the similarity of 3D structure descriptors. Here, we present a novel workflow for robust Ig 3D modeling and automated clustering. We validated our protocol in chronic...

The 3D Reference Earth Model: Status and Preliminary Results

Science.gov (United States)

Moulik, P.; Lekic, V.; Romanowicz, B. A.

2017-12-01

In the 20th century, seismologists constructed models of how average physical properties (e.g. density, rigidity, compressibility, anisotropy) vary with depth in the Earth's interior. These one-dimensional (1D) reference Earth models (e.g. PREM) have proven indispensable in earthquake location, imaging of interior structure, understanding material properties under extreme conditions, and as a reference in other fields, such as particle physics and astronomy. Over the past three decades, new datasets motivated more sophisticated efforts that yielded models of how properties vary both laterally and with depth in the Earth's interior. Though these three-dimensional (3D) models exhibit compelling similarities at large scales, differences in the methodology, representation of structure, and dataset upon which they are based, have prevented the creation of 3D community reference models. As part of the REM-3D project, we are compiling and reconciling reference seismic datasets of body wave travel-time measurements, fundamental mode and overtone surface wave dispersion measurements, and normal mode frequencies and splitting functions. These reference datasets are being inverted for a long-wavelength, 3D reference Earth model that describes the robust long-wavelength features of mantle heterogeneity. As a community reference model with fully quantified uncertainties and tradeoffs and an associated publically available dataset, REM-3D will facilitate Earth imaging studies, earthquake characterization, inferences on temperature and composition in the deep interior, and be of improved utility to emerging scientific endeavors, such as neutrino geoscience. Here, we summarize progress made in the construction of the reference long period dataset and present a preliminary version of REM-3D in the upper-mantle. In order to determine the level of detail warranted for inclusion in REM-3D, we analyze the spectrum of discrepancies between models inverted with different subsets of the

CityGML - Interoperable semantic 3D city models

Science.gov (United States)

Gröger, Gerhard; Plümer, Lutz

2012-07-01

CityGML is the international standard of the Open Geospatial Consortium (OGC) for the representation and exchange of 3D city models. It defines the three-dimensional geometry, topology, semantics and appearance of the most relevant topographic objects in urban or regional contexts. These definitions are provided in different, well-defined Levels-of-Detail (multiresolution model). The focus of CityGML is on the semantical aspects of 3D city models, its structures, taxonomies and aggregations, allowing users to employ virtual 3D city models for advanced analysis and visualization tasks in a variety of application domains such as urban planning, indoor/outdoor pedestrian navigation, environmental simulations, cultural heritage, or facility management. This is in contrast to purely geometrical/graphical models such as KML, VRML, or X3D, which do not provide sufficient semantics. CityGML is based on the Geography Markup Language (GML), which provides a standardized geometry model. Due to this model and its well-defined semantics and structures, CityGML facilitates interoperable data exchange in the context of geo web services and spatial data infrastructures. Since its standardization in 2008, CityGML has become used on a worldwide scale: tools from notable companies in the geospatial field provide CityGML interfaces. Many applications and projects use this standard. CityGML is also having a strong impact on science: numerous approaches use CityGML, particularly its semantics, for disaster management, emergency responses, or energy-related applications as well as for visualizations, or they contribute to CityGML, improving its consistency and validity, or use CityGML, particularly its different Levels-of-Detail, as a source or target for generalizations. This paper gives an overview of CityGML, its underlying concepts, its Levels-of-Detail, how to extend it, its applications, its likely future development, and the role it plays in scientific research. Furthermore, its

The 3D-city model

DEFF Research Database (Denmark)

Holmgren, Steen; Rüdiger, Bjarne; Tournay, Bruno

2001-01-01

We have worked with the construction and use of 3D city models for about ten years. This work has given us valuable experience concerning model methodology. In addition to this collection of knowledge, our perception of the concept of city models has changed radically. In order to explain...... of 3D city models....

New boundary conditions for 3D RF modelling

International Nuclear Information System (INIS)

Ko, K.; Nelson, E.; Fitze, H.

1990-01-01

The new capabilities are being implemented into the 3D particle-in-cell code, ARGUS, which will reduce substantially both problem size and computing time when modeling realistic geometries with high accuracies. In the time domain, a cylindrical radiative boundary condition will enable traveling wave propagation to be simulated in accelerator structures. An application of interest is the input coupler in the SLAC x-band high-gradient structure where local field gradients and impedance matching are important issues. In the frequency domain, a quasi-periodic boundary condition will facilitate the cold-test analysis of 3D periodic structures where many calculations are required to generate an ω β diagram. Present applications include the crossed-field amplifier cavity and the cluster klystron cavity

Modeling real conditions of 'Ukrytie' object in 3D measurement

International Nuclear Information System (INIS)

Podbereznyj, S.S.

2001-01-01

The article covers a technology of creation on soft products basis for designing: AutoCad, and computer graphics and animation 3D Studio, 3DS MAX, of 3D model of geometrical parameters of current conditions of building structures, technological equipment, fuel-containing materials, concrete, water of ruined Unit 4, 'Ukryttia' object, of Chernobyl NPP. The model built using the above technology will be applied in the future as a basis when automating the design and computer modeling of processes at the 'Ukryttia' object

Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing

Science.gov (United States)

Griffith, Kaitlyn M.; de Cataldo, Riccardo; Fogarty, Keir H.

2016-01-01

Introductory chemistry students often have difficulty visualizing the 3-dimensional shapes of the hydrogenic electron orbitals without the aid of physical 3D models. Unfortunately, commercially available models can be quite expensive. 3D printing offers a solution for producing models of hydrogenic orbitals. 3D printing technology is widely…

Radiosity diffusion model in 3D

Science.gov (United States)

Riley, Jason D.; Arridge, Simon R.; Chrysanthou, Yiorgos; Dehghani, Hamid; Hillman, Elizabeth M. C.; Schweiger, Martin

2001-11-01

We present the Radiosity-Diffusion model in three dimensions(3D), as an extension to previous work in 2D. It is a method for handling non-scattering spaces in optically participating media. We present the extension of the model to 3D including an extension to the model to cope with increased complexity of the 3D domain. We show that in 3D more careful consideration must be given to the issues of meshing and visibility to model the transport of light within reasonable computational bounds. We demonstrate the model to be comparable to Monte-Carlo simulations for selected geometries, and show preliminary results of comparisons to measured time-resolved data acquired on resin phantoms.

3D velocity structure of upper crust beneath NW Bohemia/Vogtland

Science.gov (United States)

Javad Fallahi, Mohammad; Mousavi, Sima; Korn, Michael; Sens-Schönfelder, Christoph; Bauer, Klaus; Rößler, Dirk

2013-04-01

The 3D structure of the upper crust beneath west Bohemia/Vogtland region, analyzed with travel time tomography and ambient noise surface wave tomography using existing data. This region is characterized by a series of phenomena like occurrence of repeated earthquake swarms, surface exhalation, CO2 enriched fluids, mofettes, mineral springs and enhanced heat flow, and has been proposed as an excellent location for an ICDP drilling project targeted to a better understanding of the crust in an active magmatic environment. We performed a 3D tomography using P-and S-wave travel times of local earthquakes and explosions. The data set were taken from permanent and temporary seismic networks in Germany and Czech Republic from 2000 to 2010, as well as active seismic experiments like Celebration 2000 and quarry blasts. After picking P and S wave arrival times, 399 events which were recorded by 9 or more stations and azimuthal gap<160° were selected for inversion. A simultaneous inversion of P and S wave 1D velocity models together with relocations of hypocenters and station corrections was performed. The obtained minimum 1D velocity model was used as starting model for the 3D Vp and Vp/Vs velocity models. P and S wave travel time tomography employs damped least-square method and ray tracing by pseudo-bending algorithm. For model parametrization different cell node spacings have been tested to evaluate the resolution in each node. Synthetic checkerboard tests have been done to check the structural resolution. Then Vp and Vp/Vs in the preferred 3D grid model have been determined. Earthquakes locations in iteration process change till the hypocenter adjustments and travel time residuals become smaller than the defined threshold criteria. Finally the analysis of the resolution depicts the well resolved features for interpretation. We observed lower Vp/Vs ratio in depth of 5-10 km close to the foci of earthquake swarms and higher Vp/Vs ratio is observed in Saxoturingian zone and

VP-Nets : Efficient automatic localization of key brain structures in 3D fetal neurosonography.

Science.gov (United States)

Huang, Ruobing; Xie, Weidi; Alison Noble, J

2018-04-23

Three-dimensional (3D) fetal neurosonography is used clinically to detect cerebral abnormalities and to assess growth in the developing brain. However, manual identification of key brain structures in 3D ultrasound images requires expertise to perform and even then is tedious. Inspired by how sonographers view and interact with volumes during real-time clinical scanning, we propose an efficient automatic method to simultaneously localize multiple brain structures in 3D fetal neurosonography. The proposed View-based Projection Networks (VP-Nets), uses three view-based Convolutional Neural Networks (CNNs), to simplify 3D localizations by directly predicting 2D projections of the key structures onto three anatomical views. While designed for efficient use of data and GPU memory, the proposed VP-Nets allows for full-resolution 3D prediction. We investigated parameters that influence the performance of VP-Nets, e.g. depth and number of feature channels. Moreover, we demonstrate that the model can pinpoint the structure in 3D space by visualizing the trained VP-Nets, despite only 2D supervision being provided for a single stream during training. For comparison, we implemented two other baseline solutions based on Random Forest and 3D U-Nets. In the reported experiments, VP-Nets consistently outperformed other methods on localization. To test the importance of loss function, two identical models are trained with binary corss-entropy and dice coefficient loss respectively. Our best VP-Net model achieved prediction center deviation: 1.8 ± 1.4 mm, size difference: 1.9 ± 1.5 mm, and 3D Intersection Over Union (IOU): 63.2 ± 14.7% when compared to the ground truth. To make the whole pipeline intervention free, we also implement a skull-stripping tool using 3D CNN, which achieves high segmentation accuracy. As a result, the proposed processing pipeline takes a raw ultrasound brain image as input, and output a skull-stripped image with five detected key brain

Simulating the 3-D Structure of Titan's Upper Atmosphere

Science.gov (United States)

Bell, J. M.; Waite, H.; Westlake, J.; Magee, B.

2009-05-01

We present results from the 3-D Titan Global Ionosphere-Thermosphere Model (Bell et al [2009], PSS, in review). We show comparisons between simulated N2, CH4, and H2 density fields and the in-situ data from the Cassini Ion Neutral Mass Spectrometer (INMS). We describe the temperature and wind fields consistent with these density calculations. Variations with local time, longitude, and latitude will be addressed. Potential plasma heating sources can be estimated using the 1-D model of De La Haye et al [2007, 2008] and the impacts on the thermosphere of Titan can be assessed in a global sense in Titan-GITM. Lastly, we will place these findings within the context of recent work in modeling the 2-D structure of Titan's upper atmosphere (Mueller-Wodarg et al [2008]).

A linear programming approach to reconstructing subcellular structures from confocal images for automated generation of representative 3D cellular models.

Science.gov (United States)

Wood, Scott T; Dean, Brian C; Dean, Delphine

2013-04-01

This paper presents a novel computer vision algorithm to analyze 3D stacks of confocal images of fluorescently stained single cells. The goal of the algorithm is to create representative in silico model structures that can be imported into finite element analysis software for mechanical characterization. Segmentation of cell and nucleus boundaries is accomplished via standard thresholding methods. Using novel linear programming methods, a representative actin stress fiber network is generated by computing a linear superposition of fibers having minimum discrepancy compared with an experimental 3D confocal image. Qualitative validation is performed through analysis of seven 3D confocal image stacks of adherent vascular smooth muscle cells (VSMCs) grown in 2D culture. The presented method is able to automatically generate 3D geometries of the cell's boundary, nucleus, and representative F-actin network based on standard cell microscopy data. These geometries can be used for direct importation and implementation in structural finite element models for analysis of the mechanics of a single cell to potentially speed discoveries in the fields of regenerative medicine, mechanobiology, and drug discovery. Copyright © 2012 Elsevier B.V. All rights reserved.

Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

International Nuclear Information System (INIS)

Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

2002-01-01

The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

Comparing a quasi-3D to a full 3D nearshore circulation model: SHORECIRC and ROMS

Science.gov (United States)

Haas, Kevin A.; Warner, John C.

2009-01-01

Predictions of nearshore and surf zone processes are important for determining coastal circulation, impacts of storms, navigation, and recreational safety. Numerical modeling of these systems facilitates advancements in our understanding of coastal changes and can provide predictive capabilities for resource managers. There exists many nearshore coastal circulation models, however they are mostly limited or typically only applied as depth integrated models. SHORECIRC is an established surf zone circulation model that is quasi-3D to allow the effect of the variability in the vertical structure of the currents while maintaining the computational advantage of a 2DH model. Here we compare SHORECIRC to ROMS, a fully 3D ocean circulation model which now includes a three dimensional formulation for the wave-driven flows. We compare the models with three different test applications for: (i) spectral waves approaching a plane beach with an oblique angle of incidence; (ii) monochromatic waves driving longshore currents in a laboratory basin; and (iii) monochromatic waves on a barred beach with rip channels in a laboratory basin. Results identify that the models are very similar for the depth integrated flows and qualitatively consistent for the vertically varying components. The differences are primarily the result of the vertically varying radiation stress utilized by ROMS and the utilization of long wave theory for the radiation stress formulation in vertical varying momentum balance by SHORECIRC. The quasi-3D model is faster, however the applicability of the fully 3D model allows it to extend over a broader range of processes, temporal, and spatial scales.

3D modeling of genome macroorganization on the basis of its structural changes after action of radiation

International Nuclear Information System (INIS)

Aleksandrov, I.D.; Aleksandrova, M.V.; Zaikin, N.S.; Koren'kov, V.V.; Pervushova, O.V.; Stepanenko, V.A.

2006-01-01

At present, after 120 years of the theoretical and experimental works, the issue of the genome macroarchitecture as the highest level of interphase chromosome organization in somatic cell nuclei remains still unresolved. The problem of the spatial arrangement of interphase chromosomes in haploid germ cells has never even been studied. A 3D simulation of packaging of the entire second chromosome in Drosophila mature sperms has been performed by using mathematical approaches and visualization methods to present macromolecular structure data. As genetic markers for simulation, frequency and location of the second inversion breakpoints for 72 structural υg mutants induced by ionizing radiation were used supposing that both ends of each inversion are topologically brought together forming loop of appropriate size. For the account of a degree of spatial affinity and visualization of chromosomal loops modern 3D-modeling methods with application of splines, libraries OpenGL, language Delphi, program Gmax were used. According to the model proposed, the entire second chromosome within mature sperm nuclei seems to be packaged in the form of a megarosette-loop structure which may be a basic principle of organization of the genome macro-architecture in animal haploid germ cells

Exploring structures of the Rochefort Cave (Belgium) with 3D models from LIDAR scans and UAV photoscans.

Science.gov (United States)

Watlet, A.; Triantafyllou, A.; Kaufmann, O.; Le Mouelic, S.

2016-12-01

Amongst today's techniques that are able to produce 3D point clouds, LIDAR and UAV (Unmanned Aerial Vehicle) photogrammetry are probably the most commonly used. Both methods have their own advantages and limitations. LIDAR scans create high resolution and high precision 3D point clouds, but such methods are generally costly, especially for sporadic surveys. Compared to LIDAR, UAV (e.g. drones) are cheap and flexible to use in different types of environments. Moreover, the photogrammetric processing workflow of digital images taken with UAV becomes easier with the rise of many affordable software packages (e.g., Agisoft PhotoScan, MicMac, VisualSFM). In this canvas, we present a challenging study made at the Rochefort Cave Laboratory (South Belgium) comprising surface and underground surveys. The main chamber of the cave ( 10000 m³) was the principal target of the study. A LIDAR scan and an UAV photoscan were acquired underground, producing respective 3D models. An additional 3D photoscan was performed at the surface, in the sinkhole in direct connection with the main chamber. The main goal of the project is to combine this different datasets for quantifying the orientation of inaccessible geological structures (e.g. faults, tectonic and gravitational joints, and sediments bedding), and for comparing them to structural data surveyed on the field. To go through structural interpretations, we used a subsampling method merging neighboured model polygons that have similar orientations, allowing statistical analyses of polygons spatial distribution. The benefit of this method is to verify the spatial continuity of in-situ structural measurements to larger scale. Roughness and colorimetric/spectral analyses may also be of great interest for several geosciences purposes by discriminating different facies among the geological beddings. Amongst others, this study was helpful to precise the local petrophysical properties associated with particular geological layers, what

Case study of the 3D model in ANGRA 3 project

International Nuclear Information System (INIS)

Faloppa, Altair A.; Elias, Marcos V.

2015-01-01

The 3D modeling has been increasingly used in NPP - Nuclear Power Plant from its design to its life cycle management. This paper presents experiences and developments regarding the methods applied for 3D Model in the Angra 3 NPP design using proprietary software PDS® - Plant Design System, and complementary in-house software developed by ETN. A description of the adopted methodology in all disciplines such as piping, piping support, equipment, civil, steel structure, HVAC and electrical will be detailed. The PDS® system is a comprehensive, intelligent computer-aided design/engineering application for plant design, construction, and operations. The use of PDS® and the developed tools has resulted in optimization in the design process as well as the project execution. After the design phase during the erection, commissioning and start-up of the plant, the 3D Model will be strongly helpful to obtain basic data about plant components such as piping, supports, valves, equipment and pumps. They can be easily found, opened, visualized and their properties analyzed in seconds. A corresponding data-base can also provide several different information queries. Furthermore the detailed 3D Model in the as-built condition can be used during operation and in-service inspections, reducing maintenance costs and improving safety of workers. It can also be used as an additional tool in training new operators.(author)

Case study of the 3D model in ANGRA 3 project

Energy Technology Data Exchange (ETDEWEB)

Faloppa, Altair A., E-mail: afaloppa@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil); Elias, Marcos V., E-mail: mvelias@eletronuclear.gov.br [Eletrobras Termonuclear S.A. (ELETRONUCLEAR), Rio de Janeiro, RJ (Brazil). Departamento GTP-T; Widuch, Lutzian, E-mail: Lutzian.Widuch@areva.com [AREVA GmbH, Engineering Methods and CAD Tools, Erlangen (Germany)

2015-07-01

The 3D modeling has been increasingly used in NPP - Nuclear Power Plant from its design to its life cycle management. This paper presents experiences and developments regarding the methods applied for 3D Model in the Angra 3 NPP design using proprietary software PDS® - Plant Design System, and complementary in-house software developed by ETN. A description of the adopted methodology in all disciplines such as piping, piping support, equipment, civil, steel structure, HVAC and electrical will be detailed. The PDS® system is a comprehensive, intelligent computer-aided design/engineering application for plant design, construction, and operations. The use of PDS® and the developed tools has resulted in optimization in the design process as well as the project execution. After the design phase during the erection, commissioning and start-up of the plant, the 3D Model will be strongly helpful to obtain basic data about plant components such as piping, supports, valves, equipment and pumps. They can be easily found, opened, visualized and their properties analyzed in seconds. A corresponding data-base can also provide several different information queries. Furthermore the detailed 3D Model in the as-built condition can be used during operation and in-service inspections, reducing maintenance costs and improving safety of workers. It can also be used as an additional tool in training new operators.(author)

Construction of a 3-D anatomical model for teaching temporal lobectomy.

Science.gov (United States)

de Ribaupierre, Sandrine; Wilson, Timothy D

2012-06-01

Although we live and work in 3 dimensional space, most of the anatomical teaching during medical school is done on 2-D (books, TV and computer screens, etc). 3-D spatial abilities are essential for a surgeon but teaching spatial skills in a non-threatening and safe educational environment is a much more difficult pedagogical task. Currently, initial anatomical knowledge formation or specific surgical anatomy techniques, are taught either in the OR itself, or in cadaveric labs; which means that the trainee has only limited exposure. 3-D computer models incorporated into virtual learning environments may provide an intermediate and key step in a blended learning approach for spatially challenging anatomical knowledge formation. Specific anatomical structures and their spatial orientation can be further clinically contextualized through demonstrations of surgical procedures in the 3-D digital environments. Recordings of digital models enable learner reviews, taking as much time as they want, stopping the demonstration, and/or exploring the model to understand the anatomical relation of each structure. We present here how a temporal lobectomy virtual model has been developed to aid residents and fellows conceptualization of the anatomical relationships between different cerebral structures during that procedure. We suggest in comparison to cadaveric dissection, such virtual models represent a cost effective pedagogical methodology providing excellent support for anatomical learning and surgical technique training. Copyright © 2012 Elsevier Ltd. All rights reserved.

Automatic Generation of Structural Building Descriptions from 3D Point Cloud Scans

DEFF Research Database (Denmark)

Ochmann, Sebastian; Vock, Richard; Wessel, Raoul

2013-01-01

We present a new method for automatic semantic structuring of 3D point clouds representing buildings. In contrast to existing approaches which either target the outside appearance like the facade structure or rather low-level geometric structures, we focus on the building’s interior using indoor...... scans to derive high-level architectural entities like rooms and doors. Starting with a registered 3D point cloud, we probabilistically model the affiliation of each measured point to a certain room in the building. We solve the resulting clustering problem using an iterative algorithm that relies...

3D Face Apperance Model

DEFF Research Database (Denmark)

Lading, Brian; Larsen, Rasmus; Astrom, K

2006-01-01

We build a 3D face shape model, including inter- and intra-shape variations, derive the analytical Jacobian of its resulting 2D rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations......We build a 3D face shape model, including inter- and intra-shape variations, derive the analytical Jacobian of its resulting 2D rendered image, and show example of its fitting performance with light, pose, id, expression and texture variations...

Integration of 3D photogrammetric outcrop models in the reservoir modelling workflow

Science.gov (United States)

Deschamps, Remy; Joseph, Philippe; Lerat, Olivier; Schmitz, Julien; Doligez, Brigitte; Jardin, Anne

2014-05-01

3D technologies are now widely used in geosciences to reconstruct outcrops in 3D. The technology used for the 3D reconstruction is usually based on Lidar, which provides very precise models. Such datasets offer the possibility to build well-constrained outcrop analogue models for reservoir study purposes. The photogrammetry is an alternate methodology which principles are based in determining the geometric properties of an object from photographic pictures taken from different angles. Outcrop data acquisition is easy, and this methodology allows constructing 3D outcrop models with many advantages such as: - light and fast acquisition, - moderate processing time (depending on the size of the area of interest), - integration of field data and 3D outcrops into the reservoir modelling tools. Whatever the method, the advantages of digital outcrop model are numerous as already highlighted by Hodgetts (2013), McCaffrey et al. (2005) and Pringle et al. (2006): collection of data from otherwise inaccessible areas, access to different angles of view, increase of the possible measurements, attributes analysis, fast rate of data collection, and of course training and communication. This paper proposes a workflow where 3D geocellular models are built by integrating all sources of information from outcrops (surface picking, sedimentological sections, structural and sedimentary dips…). The 3D geomodels that are reconstructed can be used at the reservoir scale, in order to compare the outcrop information with subsurface models: the detailed facies models of the outcrops are transferred into petrophysical and acoustic models, which are used to test different scenarios of seismic and fluid flow modelling. The detailed 3D models are also used to test new techniques of static reservoir modelling, based either on geostatistical approaches or on deterministic (process-based) simulation techniques. A modelling workflow has been designed to model reservoir geometries and properties from

A new 3D immersed boundary method for non-Newtonian fluid-structure-interaction with application

Science.gov (United States)

Zhu, Luoding

2017-11-01

Motivated by fluid-structure-interaction (FSI) phenomena in life sciences (e.g., motions of sperm and cytoskeleton in complex fluids), we introduce a new immersed boundary method for FSI problems involving non-Newtonian fluids in three dimensions. The non-Newtonian fluids are modelled by the FENE-P model (including the Oldroyd-B model as an especial case) and numerically solved by a lattice Boltzmann scheme (the D3Q7 model). The fluid flow is modelled by the lattice Boltzmann equations and numerically solved by the D3Q19 model. The deformable structure and the fluid-structure-interaction are handled by the immersed boundary method. As an application, we study a FSI toy problem - interaction of an elastic plate (flapped at its leading edge and restricted nowhere else) with a non-Newtonian fluid in a 3D flow. Thanks to the support of NSF-DMS support under research Grant 1522554.

Implementation and verification of interface constitutive model in FLAC3D

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Hai-min Wu

2011-09-01

Full Text Available Due to the complexity of soil-structure interaction, simple constitutive models typically used for interface elements in general computer programs cannot satisfy the requirements of discontinuous deformation analysis of structures that contain different interfaces. In order to simulate the strain-softening characteristics of interfaces, a nonlinear strain-softening interface constitutive model was incorporated into fast Lagrange analysis of continua in three dimensions (FLAC3D through a user-defined program in the FISH environment. A numerical simulation of a direct shear test for geosynthetic interfaces was conducted to verify that the interface model was implemented correctly. Results of the numerical tests show good agreement with the results obtained from theoretical calculations, indicating that the model incorporated into FLAC3D can simulate the nonlinear strain-softening behavior of interfaces involving geosynthetic materials. The results confirmed the validity and reliability of the improved interface model. The procedure and method of implementing an interface constitutive model into a commercial computer program also provide a reference for implementation of a new interface constitutive model in FLAC3D.

Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand

Science.gov (United States)

Paulino, M.; Esteves, A.; Vega, M.; Tabares, G.; Ehrlich, R.; Tapia, O.

1998-07-01

EgDf1 is a developmentally regulated protein from the parasite Echinococcus granulosus related to a family of hydrophobic ligand binding proteins. This protein could play a crucial role during the parasite life cycle development since this organism is unable to synthetize most of their own lipids de novo. Furthermore, it has been shown that two related protein from other parasitic platyhelminths (Fh15 from Fasciola hepatica and Sm14 from Schistosoma mansoni) are able to confer protective inmunity against experimental infection in animal models. A three-dimensional structure would help establishing structure/function relationships on a knowledge based manner. 3D structures for EgDf1 protein were modelled by using myelin P2 (mP2) and intestine fatty acid binding protein (I-FABP) as templates. Molecular dynamics techniques were used to validate the models. Template mP2 yielded the best 3D structure for EgDf1. Palmitic and oleic acids were docked inside EgDf1. The present theoretical results suggest definite location in the secondary structure of the epitopic regions, consensus phosphorylation motifs and oleic acid as a good ligand candidate to EgDf1. This protein might well be involved in the process of supplying hydrophobic metabolites for membrane biosynthesis and for signaling pathways.

Cation substitution studies in YBa2Cu3O7-d structure

International Nuclear Information System (INIS)

Matacotta, F.C.; Segre, C.U.; Infante, C.; Ramos Arhuis, J.; Ma, B.; Ganguly, P.

1990-04-01

The suppression of superconductivity by the substitution of divalent cations such as Sr or Ca at Y and Ba sites in Y Ba 2 Cu 3 O 7-d and the substitution of Pr for La in LaCaBaCu 3 O 7-d has been examined by ac susceptibility and infra-red spectroscopy. The latter has been found to be particularly useful in obtaining information at the microscopic level regarding the influence of substitution at the planes and at the chains. The studies give support for the model of enhancement of superconductivity by charge fluctuations in the chains. the systematics of the changes in the electrical resistivity in La 1-x Pr x CaBaCu 3 O 7-d is examined in terms of the percolation models and the existence of a minimum sheet resistance for superconductivity. The role of the various substituents in stabilizing the structure and also in the mechanism for superconductivity is examined in terms of a model for the structure of the superconducting A m Cu n O y copper oxides on the basis of AX 3 close-packing and the uniaxial magnetic interaction model. (author). 12 refs, 6 figs

Protein 3D structure computed from evolutionary sequence variation.

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Debora S Marks

Full Text Available 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 C(α-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

3D modelling for multipurpose cadastre

NARCIS (Netherlands)

Abduhl Rahman, A.; Van Oosterom, P.J.M.; Hua, T.C.; Sharkawi, K.H.; Duncan, E.E.; Azri, N.; Hassan, M.I.

2012-01-01

Three-dimensional (3D) modelling of cadastral objects (such as legal spaces around buildings, around utility networks and other spaces) is one of the important aspects for a multipurpose cadastre (MPC). This paper describes the 3D modelling of the objects for MPC and its usage to the knowledge of 3D

A novel use of 3D printing model demonstrates the effects of deteriorated trabecular bone structure on bone stiffness and strength.

Science.gov (United States)

Barak, Meir Max; Black, Margaret Arielle

2018-02-01

Trabecular bone structure is crucial to normal mechanical behavior of bones. Studies have shown that osteoporosis negatively affects trabecular bone structure, mainly by reducing bone volume fraction (BV/TV) and thus increasing fracture risk. One major limitation in assessing and quantifying the effect of this structural deterioration is that no two trabecular structures are identical. Thus, when we compare a group of healthy bones against a different group of bones that experienced resorption (i.e. decreased BV/TV) we only discover an "average" mechanical effect. It is impossible to quantify the mechanical effect of individual structural deterioration for each sample, simply because we never have the same sample in both states (intact and deteriorated structure). 3D printing is a new technology that can assist in overcoming this issue. Here we report a preliminary study that compares a healthy 3D printed trabecular bone model with the same model after bone resorption was simulated. Since the deteriorated structural bone model is derived from the healthy one, it is possible to directly estimate (percentage wise) the decrease of tissue stiffness and strength as a result of bone resorption for this specific structure. Our results demonstrate that a relatively small decrease in BV/TV (about 8%) leads to a dramatic decrease in structural strength (24%) and structural stiffness (17%), (P printing is a novel and valuable tool for quantifying the effect of structural deterioration on the mechanical properties of trabecular bone. In the future, this approach may help us attain better personal fracture risk assessments by CT scanning, 3D printing and mechanically testing individual bone replicas from patients suffering excessive bone resorption. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generating Free-Form Grid Truss Structures from 3D Scanned Point Clouds

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Hui Ding

2017-01-01

Full Text Available Reconstruction, according to physical shape, is a novel way to generate free-form grid truss structures. 3D scanning is an effective means of acquiring physical form information and it generates dense point clouds on surfaces of objects. However, generating grid truss structures from point clouds is still a challenge. Based on the advancing front technique (AFT which is widely used in Finite Element Method (FEM, a scheme for generating grid truss structures from 3D scanned point clouds is proposed in this paper. Based on the characteristics of point cloud data, the search box is adopted to reduce the search space in grid generating. A front advancing procedure suit for point clouds is established. Delaunay method and Laplacian method are used to improve the quality of the generated grids, and an adjustment strategy that locates grid nodes at appointed places is proposed. Several examples of generating grid truss structures from 3D scanned point clouds of seashells are carried out to verify the proposed scheme. Physical models of the grid truss structures generated in the examples are manufactured by 3D print, which solidifies the feasibility of the scheme.

Multiscale modeling of large deformations in 3-D polycrystals

International Nuclear Information System (INIS)

Lu Jing; Maniatty, Antoinette; Misiolek, Wojciech; Bandar, Alexander

2004-01-01

An approach for modeling 3-D polycrystals, linking to the macroscale, is presented. A Potts type model is used to generate a statistically representative grain structures with periodicity to allow scale-linking. The grain structures are compared to experimentally observed grain structures to validate that they are representative. A macroscale model of a compression test is compared against an experimental compression test for an Al-Mg-Si alloy to determine various deformation paths at different locations in the samples. These deformation paths are then applied to the experimental grain structure using a scale-bridging technique. Preliminary results from this work will be presented and discussed

Multi-view and 3D deformable part models.

Science.gov (United States)

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

2015-11-01

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

The technique for 3D printing patient-specific models for auricular reconstruction.

Science.gov (United States)

Flores, Roberto L; Liss, Hannah; Raffaelli, Samuel; Humayun, Aiza; Khouri, Kimberly S; Coelho, Paulo G; Witek, Lukasz

2017-06-01

Currently, surgeons approach autogenous microtia repair by creating a two-dimensional (2D) tracing of the unaffected ear to approximate a three-dimensional (3D) construct, a difficult process. To address these shortcomings, this study introduces the fabrication of patient-specific, sterilizable 3D printed auricular model for autogenous auricular reconstruction. A high-resolution 3D digital photograph was captured of the patient's unaffected ear and surrounding anatomic structures. The photographs were exported and uploaded into Amira, for transformation into a digital (.stl) model, which was imported into Blender, an open source software platform for digital modification of data. The unaffected auricle as digitally isolated and inverted to render a model for the contralateral side. The depths of the scapha, triangular fossa, and cymba were deepened to accentuate their contours. Extra relief was added to the helical root to further distinguish this structure. The ear was then digitally deconstructed and separated into its individual auricular components for reconstruction. The completed ear and its individual components were 3D printed using polylactic acid filament and sterilized following manufacturer specifications. The sterilized models were brought to the operating room to be utilized by the surgeon. The models allowed for more accurate anatomic measurements compared to 2D tracings, which reduced the degree of estimation required by surgeons. Approximately 20 g of the PLA filament were utilized for the construction of these models, yielding a total material cost of approximately $1. Using the methodology detailed in this report, as well as departmentally available resources (3D digital photography and 3D printing), a sterilizable, patient-specific, and inexpensive 3D auricular model was fabricated to be used intraoperatively. This technique of printing customized-to-patient models for surgeons to use as 'guides' shows great promise. Copyright © 2017 European

3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models.

Science.gov (United States)

Mai, Keith Ka Ki; Kang, Madison J; Kang, Byung-Ho

2017-01-01

Three-dimensional (3D) printing is an effective tool for preparing tangible 3D models from computer visualizations to assist in scientific research and education. With the recent popularization of 3D printing processes, it is now possible for individual laboratories to convert their scientific data into a physical form suitable for presentation or teaching purposes. Electron tomography is an electron microscopy method by which 3D structures of subcellular organelles or macromolecular complexes are determined at nanometer-level resolutions. Electron tomography analyses have revealed the convoluted membrane architectures of Golgi stacks, chloroplasts, and mitochondria. But the intricacy of their 3D organizations is difficult to grasp from tomographic models illustrated on computer screens. Despite the rapid development of 3D printing technologies, production of organelle models based on experimental data with 3D printing has rarely been documented. In this chapter, we present a simple guide to creating 3D prints of electron tomographic models of plant Golgi stacks using the two most accessible 3D printing technologies.

PENINGKATAN PENCAPAIAN KUALITAS LULUSAN D3 TEKNIK ELEKTRO DENGAN MODEL TEACHING FACTORY

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Elsanda Merita Indrawati

2017-02-01

Full Text Available The purpose of this study, namely: (1 determine systematically theimplementation of teaching factory model of the learning process D3 electrical engineering; (2 determine the achievement quality D3 graduate in electrical engineering and Teaching Factory models. The approach used is a qualitative approach, data collection techniques through observation, interviews, documentation. Results of the assessment showed that the implementation of teaching factory model of the learning process D3 Electrical Engineering done quite well, starting from the standard of competence, media, lecturers, students, use and maintenance, production, marketing, evaluation has been structured well enough. But there are still shortcomings in the establishment of management due to the formation of management, the management structure remains unclear resulted in the implementation of the model is less than the maximum teachingfactory in the Department of Electrical Engineering D3. Implementation ofteaching factory in D3 Electrical Engineering UN PGRI Kediri has been goingpretty well, the resulting product has a quality worth selling, economical and multifunctional, the students are expected after graduation in addition to be absorbed in the industrialized world are working as interpreneur and employers on the products they produce so with the application of teaching factory, the quality D3 Electrical Engineering increasing

Soil-Structure Interaction Effect on Fragility Curve of 3D Models of Concrete Moment-Resisting Buildings

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Ali Anvarsamarin

2018-01-01

Full Text Available This paper presents the probabilistic generation of collapse fragility curves for evaluating the performance of 3D, reinforced concrete (RC moment-resisting building models, considering soil-structure interaction (SSI by concentration on seismic uncertainties. It considers collapse as the loss of lateral load-resisting capacity of the building structures due to severe ground shaking and consequent large interstory drifts intensified by P-Δ effects as well as the strength and stiffness deterioration of their lateral load carrying systems. The estimation of the collapse performance of structures requires the relation between the intensity measure (IM and the probability of collapse that is determined using the generated collapse fragility curves. Considering a number of 6-, 12-, and 18-story, 3D, RC moment-resisting buildings, two scalar IMs are employed to estimate their collapse fragility curve. On the other hand, the effect of the site soil type on the collapse fragility curves was taken into account by considering the soil-structure interaction. According to the obtained results, adopting the average of spectral acceleration (Saavg intensity measure is more efficient in capturing the effect of the inherent uncertainties of the strong ground motions on the structural response parameters. In addition, considering the SSI for soil type D with shear-wave velocity of 180 m/s to 360 m/s reduces the median of intensity measure (IM = Sa(T1 of fragility curve in 6-, 12-, and 18-story buildings by 4.92%, 22.26%, and 23.03%, respectively.

3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

Energy Technology Data Exchange (ETDEWEB)

Kramar, Maxim [Physics Department, The Catholic University of America, Washington, DC (United States); Airapetian, Vladimir [Department of Physics and Astronomy, George Mason University, Fairfax, VA (United States); NASA/Goddard Space Flight Center, Code 671, Greenbelt, MD (United States); Lin, Haosheng, E-mail: vladimir.airapetian@nasa.gov [College of Natural Sciences, Institute for Astronomy, University of Hawaii at Manoa, Pukalani, HI (United States)

2016-08-09

Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131) to retrieve and analyze the three-dimensional (3D) coronal electron density in the range of heights from 1.5 to 4 R{sub ⊙} using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 Å band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below ~2.5 R{sub ⊙}. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the accuracy of the magnetic field approximations for coronal modeling.

3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

Directory of Open Access Journals (Sweden)

Maxim Kramar

2016-08-01

Full Text Available Measurement of the coronal magnetic field is a crucial ingredient in understanding the nature of solar coronal dynamic phenomena at all scales. We employ STEREO/COR1 data obtained near maximum of solar activity in December 2012 (Carrington rotation, CR 2131 to retrieve and analyze the three-dimensional (3D coronal electron density in the range of heights from $1.5$ to $4 R_odot$ using a tomography method and qualitatively deduce structures of the coronal magnetic field. The 3D electron density analysis is complemented by the 3D STEREO/EUVI emissivity in 195 AA band obtained by tomography for the same CR period. We find that the magnetic field configuration during CR 2131 has a tendency to become radially open at heliocentric distances below $sim 2.5 R_odot$. We compared the reconstructed 3D coronal structures over the CR near the solar maximum to the one at deep solar minimum. Results of our 3D density reconstruction will help to constrain solar coronal field models and test the accuracy of the magnetic field approximations for coronal modeling.

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

Science.gov (United States)

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.

Creating an Optimal 3D Printed Model for Temporal Bone Dissection Training.

Science.gov (United States)

Takahashi, Kuniyuki; Morita, Yuka; Ohshima, Shinsuke; Izumi, Shuji; Kubota, Yamato; Yamamoto, Yutaka; Takahashi, Sugata; Horii, Arata

2017-07-01

Making a 3-dimensional (3D) temporal bone model is simple using a plaster powder bed and an inkjet printer. However, it is difficult to reproduce air-containing spaces and precise middle ear structures. The objective of this study was to overcome these problems and create a temporal bone model that would be useful both as a training tool and for preoperative simulation. Drainage holes were made to remove excess materials from air-containing spaces, ossicle ligaments were manually changed to bony structures, and small and/or soft tissue structures were colored differently while designing the 3D models. The outcomes were evaluated by 3 procedures: macroscopic and endoscopic inspection of the model, comparison of computed tomography (CT) images of the model to the original CT, and assessment of tactile sensation and reproducibility by 20 surgeons performing surgery on the model. Macroscopic and endoscopic inspection, CT images, and assessment by surgeons were in agreement in terms of reproducibility of model structures. Most structures could be reproduced, but the stapes, tympanic sinus, and mastoid air cells were unsatisfactory. Perioperative tactile sensation of the model was excellent. Although this model still does not embody perfect reproducibility, it proved sufficiently practical for use in surgical training.

Shallow Crustal Structure in the Northern Salton Trough, California: Insights from a Detailed 3-D Velocity Model

Science.gov (United States)

Ajala, R.; Persaud, P.; Stock, J. M.; Fuis, G. S.; Hole, J. A.; Goldman, M.; Scheirer, D. S.

2017-12-01

The Coachella Valley is the northern extent of the Gulf of California-Salton Trough. It contains the southernmost segment of the San Andreas Fault (SAF) for which a magnitude 7.8 earthquake rupture was modeled to help produce earthquake planning scenarios. However, discrepancies in ground motion and travel-time estimates from the current Southern California Earthquake Center (SCEC) velocity model of the Salton Trough highlight inaccuracies in its shallow velocity structure. An improved 3-D velocity model that better defines the shallow basin structure and enables the more accurate location of earthquakes and identification of faults is therefore essential for seismic hazard studies in this area. We used recordings of 126 explosive shots from the 2011 Salton Seismic Imaging Project (SSIP) to SSIP receivers and Southern California Seismic Network (SCSN) stations. A set of 48,105 P-wave travel time picks constituted the highest-quality input to a 3-D tomographic velocity inversion. To improve the ray coverage, we added network-determined first arrivals at SCSN stations from 39,998 recently relocated local earthquakes, selected to a maximum focal depth of 10 km, to develop a detailed 3-D P-wave velocity model for the Coachella Valley with 1-km grid spacing. Our velocity model shows good resolution ( 50 rays/cubic km) down to a minimum depth of 7 km. Depth slices from the velocity model reveal several interesting features. At shallow depths ( 3 km), we observe an elongated trough of low velocity, attributed to sediments, located subparallel to and a few km SW of the SAF, and a general velocity structure that mimics the surface geology of the area. The persistence of the low-velocity sediments to 5-km depth just north of the Salton Sea suggests that the underlying basement surface, shallower to the NW, dips SE, consistent with interpretation from gravity studies (Langenheim et al., 2005). On the western side of the Coachella Valley, we detect depth-restricted regions of

Collaborative Multi-Scale 3d City and Infrastructure Modeling and Simulation

Science.gov (United States)

Breunig, M.; Borrmann, A.; Rank, E.; Hinz, S.; Kolbe, T.; Schilcher, M.; Mundani, R.-P.; Jubierre, J. R.; Flurl, M.; Thomsen, A.; Donaubauer, A.; Ji, Y.; Urban, S.; Laun, S.; Vilgertshofer, S.; Willenborg, B.; Menninghaus, M.; Steuer, H.; Wursthorn, S.; Leitloff, J.; Al-Doori, M.; Mazroobsemnani, N.

2017-09-01

Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future.

COLLABORATIVE MULTI-SCALE 3D CITY AND INFRASTRUCTURE MODELING AND SIMULATION

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M. Breunig

2017-09-01

Full Text Available Computer-aided collaborative and multi-scale 3D planning are challenges for complex railway and subway track infrastructure projects in the built environment. Many legal, economic, environmental, and structural requirements have to be taken into account. The stringent use of 3D models in the different phases of the planning process facilitates communication and collaboration between the stake holders such as civil engineers, geological engineers, and decision makers. This paper presents concepts, developments, and experiences gained by an interdisciplinary research group coming from civil engineering informatics and geo-informatics banding together skills of both, the Building Information Modeling and the 3D GIS world. New approaches including the development of a collaborative platform and 3D multi-scale modelling are proposed for collaborative planning and simulation to improve the digital 3D planning of subway tracks and other infrastructures. Experiences during this research and lessons learned are presented as well as an outlook on future research focusing on Building Information Modeling and 3D GIS applications for cities of the future.

Pipeline inwall 3D measurement system based on the cross structured light

Science.gov (United States)

Shen, Da; Lin, Zhipeng; Xue, Lei; Zheng, Qiang; Wang, Zichi

2014-01-01

In order to accurately realize the defect detection of pipeline inwall, this paper proposes a measurement system made up of cross structured light, single CCD camera and a smart car, etc. Based on structured light measurement technology, this paper mainly introduces the structured light measurement system, the imaging mathematical model, and the parameters and method of camera calibration. Using these measuring principles and methods, the camera in remote control car platform achieves continuous shooting of objects and real-time rebound processing as well as utilizing established model to extract 3D point cloud coordinate to reconstruct pipeline defects, so it is possible to achieve 3D automatic measuring, and verifies the correctness and feasibility of this system. It has been found that this system has great measurement accuracy in practice.

The ModFOLD4 server for the quality assessment of 3D protein models

OpenAIRE

McGuffin, Liam J.; Buenavista, Maria T.; Roche, Daniel B.

2013-01-01

Once you have generated a 3D model of a protein,\\ud how do you know whether it bears any resemblance\\ud to the actual structure? To determine the usefulness\\ud of 3D models of proteins, they must be assessed in\\ud terms of their quality by methods that predict their\\ud similarity to the native structure. The ModFOLD4\\ud server is the latest version of our leading independent\\ud server for the estimation of both the global and\\ud local (per-residue) quality of 3D protein models. The\\ud server ...

Validation of a numerical 3-D fluid-structure interaction model for a prosthetic valve based on experimental PIV measurements.

Science.gov (United States)

Guivier-Curien, Carine; Deplano, Valérie; Bertrand, Eric

2009-10-01

A numerical 3-D fluid-structure interaction (FSI) model of a prosthetic aortic valve was developed, based on a commercial computational fluid dynamics (CFD) software program using an Arbitrary Eulerian Lagrangian (ALE) formulation. To make sure of the validity of this numerical model, an equivalent experimental model accounting for both the geometrical features and the hydrodynamic conditions was also developed. The leaflet and the flow behaviours around the bileaflet valve were investigated numerically and experimentally by performing particle image velocimetry (PIV) measurements. Through quantitative and qualitative comparisons, it was shown that the leaflet behaviour and the velocity fields were similar in both models. The present study allows the validation of a fully coupled 3-D FSI numerical model. The promising numerical tool could be therefore used to investigate clinical issues involving the aortic valve.

3D modeling based on CityEngine

Science.gov (United States)

Jia, Guangyin; Liao, Kaiju

2017-03-01

Currently, there are many 3D modeling softwares, like 3DMAX, AUTOCAD, and more populous BIM softwares represented by REVIT. CityEngine modeling software introduced in this paper can fully utilize the existing GIS data and combine other built models to make 3D modeling on internal and external part of buildings in a rapid and batch manner, so as to improve the 3D modeling efficiency.

Automatic extraction of soft tissues from 3D MRI head images using model driven analysis

International Nuclear Information System (INIS)

Jiang, Hao; Yamamoto, Shinji; Imao, Masanao.

1995-01-01

This paper presents an automatic extraction system (called TOPS-3D : Top Down Parallel Pattern Recognition System for 3D Images) of soft tissues from 3D MRI head images by using model driven analysis algorithm. As the construction of system TOPS we developed, two concepts have been considered in the design of system TOPS-3D. One is the system having a hierarchical structure of reasoning using model information in higher level, and the other is a parallel image processing structure used to extract plural candidate regions for a destination entity. The new points of system TOPS-3D are as follows. (1) The TOPS-3D is a three-dimensional image analysis system including 3D model construction and 3D image processing techniques. (2) A technique is proposed to increase connectivity between knowledge processing in higher level and image processing in lower level. The technique is realized by applying opening operation of mathematical morphology, in which a structural model function defined in higher level by knowledge representation is immediately used to the filter function of opening operation as image processing in lower level. The system TOPS-3D applied to 3D MRI head images consists of three levels. First and second levels are reasoning part, and third level is image processing part. In experiments, we applied 5 samples of 3D MRI head images with size 128 x 128 x 128 pixels to the system TOPS-3D to extract the regions of soft tissues such as cerebrum, cerebellum and brain stem. From the experimental results, the system is robust for variation of input data by using model information, and the position and shape of soft tissues are extracted corresponding to anatomical structure. (author)

Formalizing Implementable Constraints in the INTERLIS Language for Modelling Legal 3D RRR Spaces and 3D Physical Objects

NARCIS (Netherlands)

Kalogianni, Eftychia; Dimopoulou, Efi; Quak, C.W.; van Oosterom, P.J.M.; van Oosterom, P.J.M.; Dimopoulou, Efi; Fendel, Elfriede M.

2016-01-01

Building Information Models (e.g. BIM, IFC) and virtual 3D city models (e.g. CityGML) are revolutionising the way we manage information about cities. The main focus of such models is on the physical and functional characteristics of urban structures (Aien et al, 2015). On the other hand cadastral

CAD CONSTRUCTION METHOD OF 3D BUILDING MODELS FOR GIS ANALYSIS

Directory of Open Access Journals (Sweden)

P. Boguslawski

2012-07-01

Full Text Available Buildings are often modelled as two-dimensional (2D footprints which are extruded to simple cubes. Buildings are also represented as more complex objects with roofs, facades, etc. – in this case they are polyhedra, sometimes of a complex shape. These allow for visualisation and analysis of a wide area like a city, but micro-scale analysis of interiors is not possible. An example can be rescue operation simulation where information about the internal structure of a building and the external terrain is crucial to improve the response time. It demands a three-dimensional (3D model where each room is represented as a separate element; there are also doors, windows, walls and other objects that have to be included. Even complex geometrical models can be easily constructed using Computer-Aided Design (CAD systems. However, lack of semantic information and topological relations makes such models poor choices for GIS analysis. With the new dual half-edge (DHE data structure and a set of Euler operators a 3D model can be built as in CAD systems, and represented as a cell complex. Construction of non-manifold objects is also possible. An advantage of the DHE is simplicity – only edges and nodes are used. Because of the 3D duality implemented in the structure volumes (cells and faces are also present in the model. The geometry of a model is constructed explicitly by using Euler operators: connections between elements are created automatically, and semantic information is represented with attributes which can be assigned to any element of the model.

Towards Precise Metadata-set for Discovering 3D Geospatial Models in Geo-portals

Science.gov (United States)

Zamyadi, A.; Pouliot, J.; Bédard, Y.

2013-09-01

Accessing 3D geospatial models, eventually at no cost and for unrestricted use, is certainly an important issue as they become popular among participatory communities, consultants, and officials. Various geo-portals, mainly established for 2D resources, have tried to provide access to existing 3D resources such as digital elevation model, LIDAR or classic topographic data. Describing the content of data, metadata is a key component of data discovery in geo-portals. An inventory of seven online geo-portals and commercial catalogues shows that the metadata referring to 3D information is very different from one geo-portal to another as well as for similar 3D resources in the same geo-portal. The inventory considered 971 data resources affiliated with elevation. 51% of them were from three geo-portals running at Canadian federal and municipal levels whose metadata resources did not consider 3D model by any definition. Regarding the remaining 49% which refer to 3D models, different definition of terms and metadata were found, resulting in confusion and misinterpretation. The overall assessment of these geo-portals clearly shows that the provided metadata do not integrate specific and common information about 3D geospatial models. Accordingly, the main objective of this research is to improve 3D geospatial model discovery in geo-portals by adding a specific metadata-set. Based on the knowledge and current practices on 3D modeling, and 3D data acquisition and management, a set of metadata is proposed to increase its suitability for 3D geospatial models. This metadata-set enables the definition of genuine classes, fields, and code-lists for a 3D metadata profile. The main structure of the proposal contains 21 metadata classes. These classes are classified in three packages as General and Complementary on contextual and structural information, and Availability on the transition from storage to delivery format. The proposed metadata set is compared with Canadian Geospatial

MolPrint3D: Enhanced 3D Printing of Ball-and-Stick Molecular Models

Science.gov (United States)

Paukstelis, Paul J.

2018-01-01

The increased availability of noncommercial 3D printers has provided instructors and students improved access to printing technology. However, printing complex ball-and-stick molecular structures faces distinct challenges, including the need for support structures that increase with molecular complexity. MolPrint3D is a software add-on for the…

Real-Time 3D Profile Measurement Using Structured Light

International Nuclear Information System (INIS)

Xu, L; Zhang, Z J; Ma, H; Yu, Y J

2006-01-01

The paper builds a real-time system of 3D profile measurement using structured-light imaging. It allows a hand-held object to rotate free in the space-time coded light field, which is projected by the projector. The surface of measured objects with projected coded light is imaged; the system shows surface reconstruction results of objects online. This feedback helps user to adjust object's pose in the light field according to the dismissed or error data, which would achieve the integrality of data used in reconstruction. This method can acquire denser data cloud and have higher reconstruction accuracy and efficiency. According to the real-time requirements, the paper presents the non-restricted light plane modelling which suits stripe structured light system, designs the three-frame stripes space-time coded pattern, and uses the advance ICP algorithms to acquire 3D data alignment from multiple view

3D for Geosciences: Interactive Tangibles and Virtual Models

Science.gov (United States)

Pippin, J. E.; Matheney, M.; Kitsch, N.; Rosado, G.; Thompson, Z.; Pierce, S. A.

2016-12-01

Point cloud processing provides a method of studying and modelling geologic features relevant to geoscience systems and processes. Here, software including Skanect, MeshLab, Blender, PDAL, and PCL are used in conjunction with 3D scanning hardware, including a Structure scanner and a Kinect camera, to create and analyze point cloud images of small scale topography, karst features, tunnels, and structures at high resolution. This project successfully scanned internal karst features ranging from small stalactites to large rooms, as well as an external waterfall feature. For comparison purposes, multiple scans of the same object were merged into single object files both automatically, using commercial software, and manually using open source libraries and code. Files with format .ply were manually converted into numeric data sets to be analyzed for similar regions between files in order to match them together. We can assume a numeric process would be more powerful and efficient than the manual method, however it could lack other useful features that GUI's may have. The digital models have applications in mining as efficient means of replacing topography functions such as measuring distances and areas. Additionally, it is possible to make simulation models such as drilling templates and calculations related to 3D spaces. Advantages of using methods described here for these procedures include the relatively quick time to obtain data and the easy transport of the equipment. With regard to openpit mining, obtaining 3D images of large surfaces and with precision would be a high value tool by georeferencing scan data to interactive maps. The digital 3D images obtained from scans may be saved as printable files to create physical 3D-printable models to create tangible objects based on scientific information, as well as digital "worlds" able to be navigated virtually. The data, models, and algorithms explored here can be used to convey complex scientific ideas to a range of

Anti-3D Weapon Model Detection for Safe 3D Printing Based on Convolutional Neural Networks and D2 Shape Distribution

Directory of Open Access Journals (Sweden)

Giao N. Pham

2018-03-01

Full Text Available With the development of 3D printing, weapons are easily printed without any restriction from the production managers. Therefore, anti-3D weapon model detection is necessary issue in safe 3D printing to prevent the printing of 3D weapon models. In this paper, we would like to propose an anti-3D weapon model detection algorithm to prevent the printing of anti-3D weapon models for safe 3D printing based on the D2 shape distribution and an improved convolutional neural networks (CNNs. The purpose of the proposed algorithm is to detect anti-3D weapon models when they are used in 3D printing. The D2 shape distribution is computed from random points on the surface of a 3D weapon model and their geometric features in order to construct a D2 vector. The D2 vector is then trained by improved CNNs. The CNNs are used to detect anti-3D weapon models for safe 3D printing by training D2 vectors which have been constructed from the D2 shape distribution of 3D weapon models. Experiments with 3D weapon models proved that the D2 shape distribution of 3D weapon models in the same class is the same. Training and testing results also verified that the accuracy of the proposed algorithm is higher than the conventional works. The proposed algorithm is applied in a small application, and it could detect anti-3D weapon models for safe 3D printing.

A 3D geological and geomechanical model of the 1963 Vajont landslide

Science.gov (United States)

Bistacchi, Andrea; Massironi, Matteo; Francese, Roberto; Giorgi, Massimo; Chistolini, Filippo; Battista Crosta, Giovanni; Castellanza, Riccardo; Frattini, Paolo; Agliardi, Federico; Frigerio, Gabriele

2014-05-01

The Vajont rockslide has been the object of several studies because of its catastrophic consequences and particular evolution. Several qualitative or quantitative models have been presented in the last 50 years, but a complete explanation of all relevant geological and mechanical processes remains elusive. In order to better understand the mechanics and dynamics of the 1963 event, we have reconstructed the first 3D geological model of the rockslide, which allowed us to accurately investigate the rockslide structure and kinematics. The input data for the model consisted in: pre- and post-rockslide geological maps, pre- and post-rockslide orthophotos, pre- and post-rockslide digital elevation models, structural data, boreholes, and geophysical data (2D and 3D seismics and resistivity). All these data have been integrated in a 3D geological model implemented in Gocad®, using the implicit surface modelling method. Results of the 3D geological model include the depth and geometry of the sliding surface, the volume of the two lobes of the rockslide accumulation, kinematics of the rockslide in terms of the vector field of finite displacement, and high quality meshes useful for mechanical and hydrogeological simulations. The latter can include information about the stratigraphy and internal structure of the rock masses and allow tracing the displacement of different material points in the rockslide from the pre-1963-failure to the post-rockslide state. As a general geological conclusion, we may say that the 3D model allowed us to recognize very effectively a sliding surface, whose non-planar geometry is affected by the interference pattern of two regional-scale fold systems. The rockslide is partitioned into two distinct and internally continuous rock masses with a distinct kinematics, which were characterised by a very limited internal deformation during the slide. The continuity of these two large blocks points to a very localized deformation, occurring along a thin

A novel 3D skin explant model to study anaerobic bacterial infection

DEFF Research Database (Denmark)

Maboni, Grazieli; Davenport, Rebecca; Sessford, Kate

2017-01-01

of the tissue structure and the cell types present in the host environment. A 3D skin culture model can be set up using tissues acquired from surgical procedures or post slaughter, making it a cost effective and attractive alternative to animal experimentation. The majority of 3D culture models have been......Skin infection studies are often limited by financial and ethical constraints, and alternatives, such as monolayer cell culture, do not reflect many cellular processes limiting their application. For a more functional replacement, 3D skin culture models offer many advantages such as the maintenance...... bacterium and the causative agent of footrot. The mechanism of infection and host immune response to D. nodosus is poorly understood. Here we present a novel 3D skin ex vivo model to study anaerobic bacterial infections using ovine skin explants infected with D. nodosus. Our results demonstrate that D...

RNA 3D modules in genome-wide predictions of RNA 2D structure

DEFF Research Database (Denmark)

Theis, Corinna; Zirbel, Craig L; Zu Siederdissen, Christian Höner

2015-01-01

. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D......Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational...... approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution...

Improvement of quality of 3D printed objects by elimination of microscopic structural defects in fused deposition modeling.

Directory of Open Access Journals (Sweden)

Evgeniy G Gordeev

Full Text Available Additive manufacturing with fused deposition modeling (FDM is currently optimized for a wide range of research and commercial applications. The major disadvantage of FDM-created products is their low quality and structural defects (porosity, which impose an obstacle to utilizing them in functional prototyping and direct digital manufacturing of objects intended to contact with gases and liquids. This article describes a simple and efficient approach for assessing the quality of 3D printed objects. Using this approach it was shown that the wall permeability of a printed object depends on its geometric shape and is gradually reduced in a following series: cylinder > cube > pyramid > sphere > cone. Filament feed rate, wall geometry and G-code-defined wall structure were found as primary parameters that influence the quality of 3D-printed products. Optimization of these parameters led to an overall increase in quality and improvement of sealing properties. It was demonstrated that high quality of 3D printed objects can be achieved using routinely available printers and standard filaments.

3D printing the pterygopalatine fossa: a negative space model of a complex structure.

Science.gov (United States)

Bannon, Ross; Parihar, Shivani; Skarparis, Yiannis; Varsou, Ourania; Cezayirli, Enis

2018-02-01

The pterygopalatine fossa is one of the most complex anatomical regions to understand. It is poorly visualized in cadaveric dissection and most textbooks rely on schematic depictions. We describe our approach to creating a low-cost, 3D model of the pterygopalatine fossa, including its associated canals and foramina, using an affordable "desktop" 3D printer. We used open source software to create a volume render of the pterygopalatine fossa from axial slices of a head computerised tomography scan. These data were then exported to a 3D printer to produce an anatomically accurate model. The resulting 'negative space' model of the pterygopalatine fossa provides a useful and innovative aid for understanding the complex anatomical relationships of the pterygopalatine fossa. This model was designed primarily for medical students; however, it will also be of interest to postgraduates in ENT, ophthalmology, neurosurgery, and radiology. The technical process described may be replicated by other departments wishing to develop their own anatomical models whilst incurring minimal costs.

A 3D visualization of spatial relationship between geological structure and groundwater chemical profile around Iwate volcano, Japan: based on the ARCGIS 3D Analyst

Science.gov (United States)

Shibahara, A.; Ohwada, M.; Itoh, J.; Kazahaya, K.; Tsukamoto, H.; Takahashi, M.; Morikawa, N.; Takahashi, H.; Yasuhara, M.; Inamura, A.; Oyama, Y.

2009-12-01

We established 3D geological and hydrological model around Iwate volcano to visualize 3D relationships between subsurface structure and groundwater profile. Iwate volcano is a typical polygenetic volcano located in NE Japan, and its body is composed of two stratovolcanoes which have experienced sector collapses several times. Because of this complex structure, groundwater flow around Iwate volcano is strongly restricted by subsurface construction. For example, Kazahaya and Yasuhara (1999) clarified that shallow groundwater in north and east flanks of Iwate volcano are recharged at the mountaintop, and these flow systems are restricted in north and east area because of the structure of younger volcanic body collapse. In addition, Ohwada et al. (2006) found that these shallow groundwater in north and east flanks have relatively high concentration of major chemical components and high 3He/4He ratios. In this study, we succeeded to visualize the spatial relationship between subsurface structure and chemical profile of shallow and deep groundwater system using 3D model on the GIS. In the study region, a number of geological and hydrological datasets, such as boring log data and groundwater chemical profile, were reported. All these paper data are digitized and converted to meshed data on the GIS, and plotted in the three dimensional space to visualize spatial distribution. We also inputted digital elevation model (DEM) around Iwate volcano issued by the Geographical Survey Institute of Japan, and digital geological maps issued by Geological Survey of Japan, AIST. All 3D models are converted into VRML format, and can be used as a versatile dataset on personal computer.

3D MODELLING OF PROPHYLACTIC FOOTWEAR FOR A HIGH ARCHED FOOT

OpenAIRE

COSTEA Mariana; MIHAI Aura

2016-01-01

This article approaches the methodology of designing customized footwear for high arched foot. The authors propose to reconsider the classical structure of footwear bottom components for people with high arched foot and recommend incorporating custom components, with the role of compensation or adjustment. This study continues the authors’ research, starting from a foot’s 3D shape obtained by 3D scanning, the anthropometrical and biomechanical parameters, shoe lasts’ 3D modelling and continui...

Monte Carlo simulation for uncertainty estimation on structural data in implicit 3-D geological modeling, a guide for disturbance distribution selection and parameterization

Science.gov (United States)

Pakyuz-Charrier, Evren; Lindsay, Mark; Ogarko, Vitaliy; Giraud, Jeremie; Jessell, Mark

2018-04-01

Three-dimensional (3-D) geological structural modeling aims to determine geological information in a 3-D space using structural data (foliations and interfaces) and topological rules as inputs. This is necessary in any project in which the properties of the subsurface matters; they express our understanding of geometries in depth. For that reason, 3-D geological models have a wide range of practical applications including but not restricted to civil engineering, the oil and gas industry, the mining industry, and water management. These models, however, are fraught with uncertainties originating from the inherent flaws of the modeling engines (working hypotheses, interpolator's parameterization) and the inherent lack of knowledge in areas where there are no observations combined with input uncertainty (observational, conceptual and technical errors). Because 3-D geological models are often used for impactful decision-making it is critical that all 3-D geological models provide accurate estimates of uncertainty. This paper's focus is set on the effect of structural input data measurement uncertainty propagation in implicit 3-D geological modeling. This aim is achieved using Monte Carlo simulation for uncertainty estimation (MCUE), a stochastic method which samples from predefined disturbance probability distributions that represent the uncertainty of the original input data set. MCUE is used to produce hundreds to thousands of altered unique data sets. The altered data sets are used as inputs to produce a range of plausible 3-D models. The plausible models are then combined into a single probabilistic model as a means to propagate uncertainty from the input data to the final model. In this paper, several improved methods for MCUE are proposed. The methods pertain to distribution selection for input uncertainty, sample analysis and statistical consistency of the sampled distribution. Pole vector sampling is proposed as a more rigorous alternative than dip vector

Monte Carlo simulation for uncertainty estimation on structural data in implicit 3-D geological modeling, a guide for disturbance distribution selection and parameterization

Directory of Open Access Journals (Sweden)

E. Pakyuz-Charrier

2018-04-01

Full Text Available Three-dimensional (3-D geological structural modeling aims to determine geological information in a 3-D space using structural data (foliations and interfaces and topological rules as inputs. This is necessary in any project in which the properties of the subsurface matters; they express our understanding of geometries in depth. For that reason, 3-D geological models have a wide range of practical applications including but not restricted to civil engineering, the oil and gas industry, the mining industry, and water management. These models, however, are fraught with uncertainties originating from the inherent flaws of the modeling engines (working hypotheses, interpolator's parameterization and the inherent lack of knowledge in areas where there are no observations combined with input uncertainty (observational, conceptual and technical errors. Because 3-D geological models are often used for impactful decision-making it is critical that all 3-D geological models provide accurate estimates of uncertainty. This paper's focus is set on the effect of structural input data measurement uncertainty propagation in implicit 3-D geological modeling. This aim is achieved using Monte Carlo simulation for uncertainty estimation (MCUE, a stochastic method which samples from predefined disturbance probability distributions that represent the uncertainty of the original input data set. MCUE is used to produce hundreds to thousands of altered unique data sets. The altered data sets are used as inputs to produce a range of plausible 3-D models. The plausible models are then combined into a single probabilistic model as a means to propagate uncertainty from the input data to the final model. In this paper, several improved methods for MCUE are proposed. The methods pertain to distribution selection for input uncertainty, sample analysis and statistical consistency of the sampled distribution. Pole vector sampling is proposed as a more rigorous alternative than

The Impacts of 3-D Earth Structure on GIA-Induced Crustal Deformation and Future Sea-Level Change in the Antarctic

Science.gov (United States)

Powell, E. M.; Hay, C.; Latychev, K.; Gomez, N. A.; Mitrovica, J. X.

2017-12-01

Glacial Isostatic Adjustment (GIA) models used to constrain the extent of past ice sheets and viscoelastic Earth structure, or to correct geodetic and geological observables for ice age effects, generally only consider depth-dependent variations in Earth viscosity and lithospheric structure. A et al. [2013] argued that 3-D Earth structure could impact GIA observables in Antarctica, but concluded that the presence of such structure contributes less to GIA uncertainty than do differences in Antarctic deglaciation histories. New seismic and geological evidence, however, indicates the Antarctic is underlain by complex, high amplitude variability in viscoelastic structure, including a low viscosity zone (LVZ) under West Antarctica. Hay et al. [2016] showed that sea-level fingerprints of modern melting calculated using such Earth models differ from those based on elastic or 1-D viscoelastic Earth models within decades of melting. Our investigation is motivated by two questions: (1) How does 3-D Earth structure, especially this LVZ, impact observations of GIA-induced crustal deformation associated with the last deglaciation? (2) How will 3-D Earth structure affect predictions of future sea-level rise in Antarctica? We compute the gravitationally self-consistent sea level, uplift, and gravity changes using the finite volume treatment of Latychev et al. [2005]. We consider four viscoelastic Earth models: a global 1-D model; a regional, West Antarctic-like 1-D model; a 3-D model where the lithospheric thickness varies laterally; and a 3-D model where both viscosity and lithospheric thickness vary laterally. For our Last Glacial Maximum to present investigations we employ ICE6g [Peltier et al., 2015]. For our present-future investigations we consider a melt scenario consistent with GRACE satellite gravity derived solutions [Harig et al., 2015]. Our calculations indicate that predictions of crustal deformations due to both GIA and ongoing melting are strongly influenced by 3-D

3D structure of muscle dihydropyridine receptor

Directory of Open Access Journals (Sweden)

Montserrat Samsó

2015-01-01

Full Text Available Excitation contraction coupling, the rapid and massive Ca2+ release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR and the ryanodine receptor (RyR1 mediates the quasi‐instantaneous conversion from T‐tubule depolarization into Ca2+ release from the sarcoplasmic reticulum (SR. The DHPR has several key modules required for EC coupling: the voltage sensors and II‐III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II‐III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data.

Engineering 3D Models of Tumors and Bone to Understand Tumor-Induced Bone Disease and Improve Treatments

Science.gov (United States)

Kwakwa, Kristin A.; Vanderburgh, Joseph P.; Guelcher, Scott A.

2018-01-01

Purpose of Review Bone is a structurally unique microenvironment that presents many challenges for the development of 3D models for studying bone physiology and diseases, including cancer. As researchers continue to investigate the interactions within the bone microenvironment, the development of 3D models of bone has become critical. Recent Findings 3D models have been developed that replicate some properties of bone, but have not fully reproduced the complex structural and cellular composition of the bone microenvironment. This review will discuss 3D models including polyurethane, silk, and collagen scaffolds that have been developed to study tumor-induced bone disease. In addition, we discuss 3D printing techniques used to better replicate the structure of bone. Summary 3D models that better replicate the bone microenvironment will help researchers better understand the dynamic interactions between tumors and the bone microenvironment, ultimately leading to better models for testing therapeutics and predicting patient outcomes. PMID:28646444

Statistical 3D damage accumulation model for ion implant simulators

CERN Document Server

Hernandez-Mangas, J M; Enriquez, L E; Bailon, L; Barbolla, J; Jaraiz, M

2003-01-01

A statistical 3D damage accumulation model, based on the modified Kinchin-Pease formula, for ion implant simulation has been included in our physically based ion implantation code. It has only one fitting parameter for electronic stopping and uses 3D electron density distributions for different types of targets including compound semiconductors. Also, a statistical noise reduction mechanism based on the dose division is used. The model has been adapted to be run under parallel execution in order to speed up the calculation in 3D structures. Sequential ion implantation has been modelled including previous damage profiles. It can also simulate the implantation of molecular and cluster projectiles. Comparisons of simulated doping profiles with experimental SIMS profiles are presented. Also comparisons between simulated amorphization and experimental RBS profiles are shown. An analysis of sequential versus parallel processing is provided.

Statistical 3D damage accumulation model for ion implant simulators

International Nuclear Information System (INIS)

Hernandez-Mangas, J.M.; Lazaro, J.; Enriquez, L.; Bailon, L.; Barbolla, J.; Jaraiz, M.

2003-01-01

A statistical 3D damage accumulation model, based on the modified Kinchin-Pease formula, for ion implant simulation has been included in our physically based ion implantation code. It has only one fitting parameter for electronic stopping and uses 3D electron density distributions for different types of targets including compound semiconductors. Also, a statistical noise reduction mechanism based on the dose division is used. The model has been adapted to be run under parallel execution in order to speed up the calculation in 3D structures. Sequential ion implantation has been modelled including previous damage profiles. It can also simulate the implantation of molecular and cluster projectiles. Comparisons of simulated doping profiles with experimental SIMS profiles are presented. Also comparisons between simulated amorphization and experimental RBS profiles are shown. An analysis of sequential versus parallel processing is provided

a Proposal for Generalization of 3d Models

Science.gov (United States)

Uyar, A.; Ulugtekin, N. N.

2017-11-01

In recent years, 3D models have been created of many cities around the world. Most of the 3D city models have been introduced as completely graphic or geometric models, and the semantic and topographic aspects of the models have been neglected. In order to use 3D city models beyond the task, a generalization is necessary. CityGML is an open data model and XML-based format for the storage and exchange of virtual 3D city models. Level of Details (LoD) which is an important concept for 3D modelling, can be defined as outlined degree or prior representation of real-world objects. The paper aim is first describes some requirements of 3D model generalization, then presents problems and approaches that have been developed in recent years. In conclude the paper will be a summary and outlook on problems and future work.

Geometric Structure of 3D Spinal Curves: Plane Regions and Connecting Zones

Science.gov (United States)

Berthonnaud, E.; Hilmi, R.; Dimnet, J.

2012-01-01

This paper presents a new study of the geometric structure of 3D spinal curves. The spine is considered as an heterogeneous beam, compound of vertebrae and intervertebral discs. The spine is modeled as a deformable wire along which vertebrae are beads rotating about the wire. 3D spinal curves are compound of plane regions connected together by zones of transition. The 3D spinal curve is uniquely flexed along the plane regions. The angular offsets between adjacent regions are concentrated at level of the middle zones of transition, so illustrating the heterogeneity of the spinal geometric structure. The plane regions along the 3D spinal curve must satisfy two criteria: (i) a criterion of minimum distance between the curve and the regional plane and (ii) a criterion controlling that the curve is continuously plane at the level of the region. The geometric structure of each 3D spinal curve is characterized by the sizes and orientations of regional planes, by the parameters representing flexed regions and by the sizes and functions of zones of transition. Spinal curves of asymptomatic subjects show three plane regions corresponding to spinal curvatures: lumbar, thoracic and cervical curvatures. In some scoliotic spines, four plane regions may be detected. PMID:25031873

The 3-dimensional core model DYN3D

Energy Technology Data Exchange (ETDEWEB)

Grundmann, U.; Mittag, S.; Rohde, U.

1999-01-01

Analyzing the safety margins in transients and accidents of nuclear reactors 3-dimensional models of the core were used to avoid conservative assumptions needed for point kinetics or 1-dimensional models. Therefore, the 3D code DYN3D has been developed for the analysis of reactivity initiated accidents (RIA) in thermal nuclear reactors. The power distributions are calculated with the help of nodal expansion methods (NEM) for hexagonal and Cartesian geometry. The fuel rod model and the thermohydraulic part provide fuel temperatures, coolant temperatures and densities as well as boron concentrations for the calculation of feedback effects on the basis of cross section libraries generated by cell codes. Safety relevant parameters like maximum fuel and cladding temperatures, critical heat flux and degree of cladding oxidation are estimated. DYN3D can analyze RIA initiated by moved control rods and/or perturbations of the coolant flow. Stationary and transient boundary conditions for the coolant flow, the core inlet temperatures and boron concentrations at the core inlet have to be given. For analyzing more complex transients the code DYN3D is coupled with the plant model ATHLET of the GRS. The extensive validation work accomplished for DYN3D is presented in several examples. Some applications of the code are described. (orig.) [Deutsch] Die Verwendung 3-dimensionaler Kernmodelle zur Untersuchung der Sicherheitsreserven bei Uebergangsprozessen und Stoerfaellen in Kernreaktoren vermeidet konservative Annahmen, die bei der Benutzung des Punktmodells oder 1-dimensionaler Modelle erforderlich sind. Aus diesen Gruenden wurde das 3-dimensionale Rechenprogramm DYN3D fuer die Untersuchung von Reaktivitaetsstoerfaellen in thermischen Reaktoren entwickelt. Die Leistungsverteilung wird mit nodalen Methoden fuer hexagonale oder kartesische Geometrie berechnet. Das Brennstabmodell und der thermohydraulische Teil von DYN3D liefert die Brennstofftemperaturen, Kuehlmitteltemperaturen

p3d--Python module for structural bioinformatics.

Science.gov (United States)

Fufezan, Christian; Specht, Michael

2009-08-21

High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

Modeling the blockage of Lg waves from 3-D variations in crustal structure

Science.gov (United States)

Sanborn, Christopher J.; Cormier, Vernon F.

2018-05-01

Comprised of S waves trapped in Earth's crust, the high frequency (2-10 Hz) Lg wave is important to discriminating earthquakes from explosions by comparing its amplitude and waveform to those of Pg and Pn waves. Lateral variations in crustal structure, including variations in crustal thickness, intrinsic attenuation, and scattering, affect the efficiency of Lg propagation and its consistency as a source discriminant at regional (200-1500 km) distances. To investigate the effects of laterally varying Earth structure on the efficiency of propagation of Lg and Pg, we apply a radiative transport algorithm to model complete, high-frequency (2-4 Hz), regional coda envelopes. The algorithm propagates packets of energy with ray theory through large-scale 3-D structure, and includes stochastic effects of multiple-scattering by small-scale heterogeneities within the large-scale structure. Source-radiation patterns are described by moment tensors. Seismograms of explosion and earthquake sources are synthesized in canonical models to predict effects on waveforms of paths crossing regions of crustal thinning (pull-apart basins and ocean/continent transitions) and thickening (collisional mountain belts), For paths crossing crustal thinning regions, Lg is amplified at receivers within the thinned region but strongly disrupted and attenuated at receivers beyond the thinned region. For paths crossing regions of crustal thickening, Lg amplitude is attenuated at receivers within the thickened region, but experiences little or no reduction in amplitude at receivers beyond the thickened region. The length of the Lg propagation within a thickened region and the complexity of over- and under-thrust crustal layers, can produce localized zones of Lg amplification or attenuation. Regions of intense scattering within laterally homogeneous models of the crust increase Lg attenuation but do not disrupt its coda shape.

Integrated geophysical and geological modelling: insights in the 3D structure and kinematics of the Hercynian Suture Zone in the Champtoceaux area (Brittany, France)

Science.gov (United States)

Martelet, G.; Calcagno, Ph.; Gumiaux, C.; Truffert, C.; Bitri, A.; Gapais, D.; Brun, J. P.

2003-04-01

Using the Editeur Géologique, a software specifically developed for the purpose of 3D geological modelling by the French Geological Survey (BRGM), we model a segment of the Hercynian suture zone of western Europe, in Champtoceaux area (Brittany, western France). The area shows exposures of strongly deformed eclogite-bearing gneisses and micaschists. These units were stacked during collision and exhumed during late Devonian to early Carboniferous times. Regional-scale dextral simple shear accompanied strike-slip movements along the SASZ (South Armorican Shear Zone). It produced a km-scale antiformal structure in the Champtoceaux metamorphic units with a steeply-dipping axial plane and a steeply eastward-plunging axis. Interpretation of the recent Armor2 seismic profile shows that the well-recognized north-dipping early lithological structuration is cross-cut by Carboniferous south-dipping inverse tectonics of crustal extension. In order to precise and extend in 3D the structures interpreted in the seismic profile, we model seven radial gravity profiles throughout Champtoceaux periclinal termination, based on data from the French gravity database. Direct 2D modelling is performed at a crustal scale, based on seismic constraints and geological field observations, as well as density measurements on samples or in drill holes. Input in the Editeur Géologique, the consistency of cross-sections, digitized geological map and structural information (foliation dips) is first checked. From the surface to the Moho, available spatialised 2D information is then interpolated in the whole 3D space using adapted geostatistical analysis. Finally, taking into account densities associated to each modelled geological body, the computation of the 3D gravity effect of the model is compared to the measured Bouguer anomaly, which insures that all complex 3D gravity effects are well taken into account. Results emphasise the usefulness of integrated geological and geophysical 3D modelling

Structured-Light Based 3d Laser Scanning of Semi-Submerged Structures

Science.gov (United States)

van der Lucht, J.; Bleier, M.; Leutert, F.; Schilling, K.; Nüchter, A.

2018-05-01

In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.

STRUCTURED-LIGHT BASED 3D LASER SCANNING OF SEMI-SUBMERGED STRUCTURES

Directory of Open Access Journals (Sweden)

J. van der Lucht

2018-05-01

Full Text Available In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.

Increasing dimension of structures by 4D printing shape memory polymers via fused deposition modeling

Science.gov (United States)

Hu, G. F.; Damanpack, A. R.; Bodaghi, M.; Liao, W. H.

2017-12-01

The main objective of this paper is to introduce a 4D printing method to program shape memory polymers (SMPs) during fabrication process. Fused deposition modeling (FDM) as a filament-based printing method is employed to program SMPs during depositing the material. This method is implemented to fabricate complicated polymeric structures by self-bending features without need of any post-programming. Experiments are conducted to demonstrate feasibility of one-dimensional (1D)-to 2D and 2D-to-3D self-bending. It is shown that 3D printed plate structures can transform into masonry-inspired 3D curved shell structures by simply heating. Good reliability of SMP programming during printing process is also demonstrated. A 3D macroscopic constitutive model is established to simulate thermo-mechanical features of the printed SMPs. Governing equations are also derived to simulate programming mechanism during printing process and shape change of self-bending structures. In this respect, a finite element formulation is developed considering von-Kármán geometric nonlinearity and solved by implementing iterative Newton-Raphson scheme. The accuracy of the computational approach is checked with experimental results. It is demonstrated that the theoretical model is able to replicate the main characteristics observed in the experiments. This research is likely to advance the state of the art FDM 4D printing, and provide pertinent results and computational tool that are instrumental in design of smart materials and structures with self-bending features.

Phononic Band Gaps in 2D Quadratic and 3D Cubic Cellular Structures.

Science.gov (United States)

Warmuth, Franziska; Körner, Carolin

2015-12-02

The static and dynamic mechanical behaviour of cellular materials can be designed by the architecture of the underlying unit cell. In this paper, the phononic band structure of 2D and 3D cellular structures is investigated. It is shown how the geometry of the unit cell influences the band structure and eventually leads to full band gaps. The mechanism leading to full band gaps is elucidated. Based on this knowledge, a 3D cellular structure with a broad full band gap is identified. Furthermore, the dependence of the width of the gap on the geometry parameters of the unit cell is presented.

Three barium diphosphonates with 3-D structures

Science.gov (United States)

Tuikka, Matti; Haukka, Matti; Ahlgrén, Markku

2007-06-01

The gel crystallization method was exploited in this work in order to study the 3-D solid state structures of barium diphosphonates. This technique proved to be an effective tool for the growth of single crystals of diphosphonates for structure analysis. By using this approach, three barium diphosphonates, Ba[HO 3P(CH 2) 2PO 3H] ( 1), Ba 2[O 3P(CH 2) 3PO 3]·3H 2O ( 2) and Ba[HO 3P(CH 2) 4PO 3H] ( 3), with different three dimensional structures, were synthesized and characterized. The structures of compounds 1 and 2 were determined by single crystal X-ray diffraction and the structure of 3 by the powder diffraction method. In the structure of 1, the diphosphonate ligand is completely surrounded by the Ba atoms, which is an unusual arrangement in a diphosphonate system. The structures of 2 and 3 are more conventional. They are organized in typical pillared layers in which the separation of the layers can be adjusted by varying the length of the hydrocarbon chain.

Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist

Energy Technology Data Exchange (ETDEWEB)

Chien, Ellen Y.T.; Liu, Wei; Zhao, Qiang; Katritch, Vsevolod; Han, Gye Won; Hanson, Michael A.; Shi, Lei; Newman, Amy Hauck; Javitch, Jonathan A.; Cherezov, Vadim; Stevens, Raymond C. (Cornell); (Scripps); (NIDA); (Columbia); (UCSD); (Receptos)

2010-11-30

Dopamine modulates movement, cognition, and emotion through activation of dopamine G protein-coupled receptors in the brain. The crystal structure of the human dopamine D3 receptor (D3R) in complex with the small molecule D2R/D3R-specific antagonist eticlopride reveals important features of the ligand binding pocket and extracellular loops. On the intracellular side of the receptor, a locked conformation of the ionic lock and two distinctly different conformations of intracellular loop 2 are observed. Docking of R-22, a D3R-selective antagonist, reveals an extracellular extension of the eticlopride binding site that comprises a second binding pocket for the aryl amide of R-22, which differs between the highly homologous D2R and D3R. This difference provides direction to the design of D3R-selective agents for treating drug abuse and other neuropsychiatric indications.

High-order finite difference solution for 3D nonlinear wave-structure interaction

DEFF Research Database (Denmark)

Ducrozet, Guillaume; Bingham, Harry B.; Engsig-Karup, Allan Peter

2010-01-01

This contribution presents our recent progress on developing an efficient fully-nonlinear potential flow model for simulating 3D wave-wave and wave-structure interaction over arbitrary depths (i.e. in coastal and offshore environment). The model is based on a high-order finite difference scheme O...

Investigations of Structural Requirements for BRD4 Inhibitors through Ligand- and Structure-Based 3D QSAR Approaches

Directory of Open Access Journals (Sweden)

Adeena Tahir

2018-06-01

Full Text Available The bromodomain containing protein 4 (BRD4 recognizes acetylated histone proteins and plays numerous roles in the progression of a wide range of cancers, due to which it is under intense investigation as a novel anti-cancer drug target. In the present study, we performed three-dimensional quantitative structure activity relationship (3D-QSAR molecular modeling on a series of 60 inhibitors of BRD4 protein using ligand- and structure-based alignment and different partial charges assignment methods by employing comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA approaches. The developed models were validated using various statistical methods, including non-cross validated correlation coefficient (r2, leave-one-out (LOO cross validated correlation coefficient (q2, bootstrapping, and Fisher’s randomization test. The highly reliable and predictive CoMFA (q2 = 0.569, r2 = 0.979 and CoMSIA (q2 = 0.500, r2 = 0.982 models were obtained from a structure-based 3D-QSAR approach using Merck molecular force field (MMFF94. The best models demonstrate that electrostatic and steric fields play an important role in the biological activities of these compounds. Hence, based on the contour maps information, new compounds were designed, and their binding modes were elucidated in BRD4 protein’s active site. Further, the activities and physicochemical properties of the designed molecules were also predicted using the best 3D-QSAR models. We believe that predicted models will help us to understand the structural requirements of BRD4 protein inhibitors that belong to quinolinone and quinazolinone classes for the designing of better active compounds.

3D virtual human rapid modeling method based on top-down modeling mechanism

Directory of Open Access Journals (Sweden)

LI Taotao

2017-01-01

Full Text Available Aiming to satisfy the vast custom-made character demand of 3D virtual human and the rapid modeling in the field of 3D virtual reality, a new virtual human top-down rapid modeling method is put for-ward in this paper based on the systematic analysis of the current situation and shortage of the virtual hu-man modeling technology. After the top-level realization of virtual human hierarchical structure frame de-sign, modular expression of the virtual human and parameter design for each module is achieved gradu-al-level downwards. While the relationship of connectors and mapping restraints among different modules is established, the definition of the size and texture parameter is also completed. Standardized process is meanwhile produced to support and adapt the virtual human top-down rapid modeling practice operation. Finally, the modeling application, which takes a Chinese captain character as an example, is carried out to validate the virtual human rapid modeling method based on top-down modeling mechanism. The result demonstrates high modelling efficiency and provides one new concept for 3D virtual human geometric mod-eling and texture modeling.

Inspiration from drones, Lidar measurements and 3D models in undergraduate teaching

Science.gov (United States)

Blenkinsop, Thomas; Ellis, Jennifer

2017-04-01

Three-dimensional models, photogrammetry and remote sensing are increasingly common techniques used in structural analysis. We have found that using drones and Lidar on undergraduate field trips has piqued interest in fieldwork, provided data for follow-up laboratory exercises, and inspired undergraduates to attempt 3D modelling in independent mapping projects. The scale of structures visible in cliff and sea shore exposures in South Wales is ideal for using drones to capture images for 3D models. Fault scarps in the South Wales coalfield were scanned by Lidar and drone. Our experience suggests that the drone data were much easier to acquire and process than the Lidar data, and adequate for most teaching purposes. In the lab, we used the models to show the structure in 3D, and as the basis for an introduction to geological modelling software. Now that tools for photogrammetry, drones, and processing software are widely available and affordable, they can be readily integrated into teaching. An additional benefit from the images and models is that they may be used for exercises that can be substituted for fieldwork to achieve some (but not all) of the learning outcomes in the case that field access is prevented.

3D-printing and mechanics of bio-inspired articulated and multi-material structures.

Science.gov (United States)

Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

2017-09-01

3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic. Copyright © 2017 Elsevier Ltd. All rights reserved.

Virtual 3d City Modeling: Techniques and Applications

Science.gov (United States)

Singh, S. P.; Jain, K.; Mandla, V. R.

2013-08-01

3D city model is a digital representation of the Earth's surface and it's related objects such as Building, Tree, Vegetation, and some manmade feature belonging to urban area. There are various terms used for 3D city models such as "Cybertown", "Cybercity", "Virtual City", or "Digital City". 3D city models are basically a computerized or digital model of a city contains the graphic representation of buildings and other objects in 2.5 or 3D. Generally three main Geomatics approach are using for Virtual 3-D City models generation, in first approach, researcher are using Conventional techniques such as Vector Map data, DEM, Aerial images, second approach are based on High resolution satellite images with LASER scanning, In third method, many researcher are using Terrestrial images by using Close Range Photogrammetry with DSM & Texture mapping. We start this paper from the introduction of various Geomatics techniques for 3D City modeling. These techniques divided in to two main categories: one is based on Automation (Automatic, Semi-automatic and Manual methods), and another is Based on Data input techniques (one is Photogrammetry, another is Laser Techniques). After details study of this, finally in short, we are trying to give the conclusions of this study. In the last, we are trying to give the conclusions of this research paper and also giving a short view for justification and analysis, and present trend for 3D City modeling. This paper gives an overview about the Techniques related with "Generation of Virtual 3-D City models using Geomatics Techniques" and the Applications of Virtual 3D City models. Photogrammetry, (Close range, Aerial, Satellite), Lasergrammetry, GPS, or combination of these modern Geomatics techniques play a major role to create a virtual 3-D City model. Each and every techniques and method has some advantages and some drawbacks. Point cloud model is a modern trend for virtual 3-D city model. Photo-realistic, Scalable, Geo-referenced virtual 3

Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.

Science.gov (United States)

Han, Xusi; Wei, Qing; Kihara, Daisuke

2017-12-08

With the rapid growth in the number of solved protein structures stored in the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB), it is essential to develop tools to perform real-time structure similarity searches against the entire structure database. Since conventional structure alignment methods need to sample different orientations of proteins in the three-dimensional space, they are time consuming and unsuitable for rapid, real-time database searches. To this end, we have developed 3D-SURFER and EM-SURFER, which utilize 3D Zernike descriptors (3DZD) to conduct high-throughput protein structure comparison, visualization, and analysis. Taking an atomic structure or an electron microscopy map of a protein or a protein complex as input, the 3DZD of a query protein is computed and compared with the 3DZD of all other proteins in PDB or EMDB. In addition, local geometrical characteristics of a query protein can be analyzed using VisGrid and LIGSITE CSC in 3D-SURFER. This article describes how to use 3D-SURFER and EM-SURFER to carry out protein surface shape similarity searches, local geometric feature analysis, and interpretation of the search results. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Towards a 3d Spatial Urban Energy Modelling Approach

Science.gov (United States)

Bahu, J.-M.; Koch, A.; Kremers, E.; Murshed, S. M.

2013-09-01

Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies

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

Science.gov (United States)

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.

The Esri 3D city information model

International Nuclear Information System (INIS)

Reitz, T; Schubiger-Banz, S

2014-01-01

With residential and commercial space becoming increasingly scarce, cities are going vertical. Managing the urban environments in 3D is an increasingly important and complex undertaking. To help solving this problem, Esri has released the ArcGIS for 3D Cities solution. The ArcGIS for 3D Cities solution provides the information model, tools and apps for creating, analyzing and maintaining a 3D city using the ArcGIS platform. This paper presents an overview of the 3D City Information Model and some sample use cases

PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.

Directory of Open Access Journals (Sweden)

Radhakrishna Bettadapura

2015-10-01

Full Text Available There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data, and 3D reconstructed cryo-electron microscopy (3D EM maps (albeit at coarser resolution of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2 fit (Polar Fast Fourier Fitting for the best possible structural alignment of atomistic structures with 3D EM. While PF(2 fit enables only a rigid, six dimensional (6D alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.

Access to the kinematic information for the velocity model determination by 3-D reflexion tomography; Acces a l'information cinematique pour la determination du modele de vitesse par tomographie de reflexion 3D

Energy Technology Data Exchange (ETDEWEB)

Broto, K.

1999-04-01

The access to a reliable image of the subsurface requires a kinematically correct velocity depth model.Reflection tomography allows to meet this requirement if a complete and coherent pre-stack kinematic database can be provided. However, in case of complex sub-surfaces, wave propagation may lead to hardly interpretable seismic events in the time data. The SMART method is a sequential method that relies on reflection tomography for updating the velocity model and on the pre-stack depth migrated domain for extracting kinematic information that is not readily accessible in the time domain. For determining 3-D subsurface velocity models in case of complex structures, we propose the seriated SMART 2-D method as an alternative to the currently inconceivable SMART 3-D method. In order to extract kinematic information from a 3-D pre-stack data set, we combine detours through the 2-D pre-stack depth domain for a number of selected lines of the studied 3-D survey and 3-D reflection tomography for updating the velocity model. The travel-times from the SMART method being independent of the velocity model used for passing through the pre-stack depth migrated domain, the access to 3-D travel-times is ensured, even if they have been obtained via a 2-D domain. Besides, we propose to build a kinematical guide for ensuring the coherency of the seriated 2-D pre-stack depth interpretations and the access to a complete 3-D pre-stack kinematic database when dealing with structures associated with 3-D wave propagation. We opt for a blocky representation of the velocity model in order to be able to cope with complex structures. This representation leads us to define specific methodological rules for carrying out the different steps of the seriated SMART 2-D method. We also define strategies, built from the analysis of first inversion results, for an efficient application of reflection tomography. Besides, we discuss the problem of uncertainties to be assigned to travel-times obtained

Rapid fabrication of 2D and 3D photonic crystals and their inversed structures

International Nuclear Information System (INIS)

Huang, C-K; Chan, C-H; Chen, C-Y; Tsai, Y-L; Chen, C-C; Han, J-L; Hsieh, K-H

2007-01-01

In this paper a new technique is proposed for the fabrication of two-dimensional (2D) and three-dimensional (3D) photonic crystals using monodisperse polystyrene microspheres as the templates. In addition, the approaches toward the creation of their corresponding inversed structures are described. The inversed structures were prepared by subjecting an introduced silica source to a sol-gel process; programmed heating was then performed to remove the template without spoiling the inversed structures. Utilizing these approaches, 2D and 3D photonic crystals and their highly ordered inversed hexagonal multilayer or monolayer structures were obtained on the substrate

Quantifying Multiscale Habitat Structural Complexity: A Cost-Effective Framework for Underwater 3D Modelling

Directory of Open Access Journals (Sweden)

Renata Ferrari

2016-02-01

Full Text Available Coral reef habitat structural complexity influences key ecological processes, ecosystem biodiversity, and resilience. Measuring structural complexity underwater is not trivial and researchers have been searching for accurate and cost-effective methods that can be applied across spatial extents for over 50 years. This study integrated a set of existing multi-view, image-processing algorithms, to accurately compute metrics of structural complexity (e.g., ratio of surface to planar area underwater solely from images. This framework resulted in accurate, high-speed 3D habitat reconstructions at scales ranging from small corals to reef-scapes (10s km2. Structural complexity was accurately quantified from both contemporary and historical image datasets across three spatial scales: (i branching coral colony (Acropora spp.; (ii reef area (400 m2; and (iii reef transect (2 km. At small scales, our method delivered models with <1 mm error over 90% of the surface area, while the accuracy at transect scale was 85.3% ± 6% (CI. Advantages are: no need for an a priori requirement for image size or resolution, no invasive techniques, cost-effectiveness, and utilization of existing imagery taken from off-the-shelf cameras (both monocular or stereo. This remote sensing method can be integrated to reef monitoring and improve our knowledge of key aspects of coral reef dynamics, from reef accretion to habitat provisioning and productivity, by measuring and up-scaling estimates of structural complexity.

Conforming to interface structured adaptive mesh refinement: 3D algorithm and implementation

Science.gov (United States)

Nagarajan, Anand; Soghrati, Soheil

2018-03-01

A new non-iterative mesh generation algorithm named conforming to interface structured adaptive mesh refinement (CISAMR) is introduced for creating 3D finite element models of problems with complex geometries. CISAMR transforms a structured mesh composed of tetrahedral elements into a conforming mesh with low element aspect ratios. The construction of the mesh begins with the structured adaptive mesh refinement of elements in the vicinity of material interfaces. An r-adaptivity algorithm is then employed to relocate selected nodes of nonconforming elements, followed by face-swapping a small fraction of them to eliminate tetrahedrons with high aspect ratios. The final conforming mesh is constructed by sub-tetrahedralizing remaining nonconforming elements, as well as tetrahedrons with hanging nodes. In addition to studying the convergence and analyzing element-wise errors in meshes generated using CISAMR, several example problems are presented to show the ability of this method for modeling 3D problems with intricate morphologies.

A full 3D time-dependent electromagnetic model for Roebel cables

DEFF Research Database (Denmark)

Rodriguez Zermeno, Victor Manuel; Grilli, Francesco; Sirois, Frederic

2013-01-01

High temperature superconductor Roebel cables are well known for their large current capacity and low AC losses. For this reason they have become attractive candidates for many power applications. The continuous transposition of their strands reduces the coupling losses while ensuring better...... is unavoidably a large scale computational problem. In this work, we present a full 3D model of a Roebel cable with 14 strands. The model is based on the H-formulation, widely used for 2D problems. In order to keep the 3D features of the cable (in particular the magnetization currents near the transpositions......), no simplifications are made other than the reduction of the modelled length according to the periodicity of the cable structure. The 3D model is used to study the dependence of AC losses on the amplitude of the AC applied magnetic field or transport current. Beyond the importance of simulating the Roebel cable...

Hyperfine structure in 5s4d 3D-5snf transitions of 87Sr

International Nuclear Information System (INIS)

Bushaw, B.A.; Kluge, H.J.; Lantzsch, J.; Schwalbach, R.; Stenner, J.; Stevens, H.; Wendt, K.; Zimmer, K.

1993-01-01

The hyperfine spectra of the 5s4d 3 D 1 -5s20f, 5s4d 3 D 2 -5s23f, and 5s4d 3 D 3 -5s32f transitions of 87 Sr (I=9/2) have been measured by collinear fast beam laser spectroscopy. The structure in the upper configurations is highly perturbed by fine structure splitting that is of comparable size to the hyperfine interaction energy. These perturbations can be adequately treated with conventional matrix diagonalization methods, using the 5s-electron magnetic dipole interaction term a 5s and the unperturbed fine structure splittings as input parameters. Additionally, hyperfine constants for the lower 5s4d 3 D configurations, including the A- and B-factors and a separation of the individual s- and d-electron contributions to these factors, are derived. (orig.)

3D-modeling and 3D-printing explorations on Japanese tea ceremony utensils

NARCIS (Netherlands)

Levy, P.D.; Yamada, Shigeru

2017-01-01

In this paper, we inquire aesthetical aspects of the Japanese tea ceremony, described as the aesthetics in the imperfection, based on novel fabrication technologies: 3D-modeling and 3D-printing. To do so, 3D-printed utensils (chashaku and chasen) were iteratively designed for the ceremony and were

The Traveling Optical Scanner – Case Study on 3D Shape Models of Ancient Brazilian Skulls

DEFF Research Database (Denmark)

Trinderup, Camilla Himmelstrup; Dahl, Vedrana Andersen; Gregersen, Kristian Murphy

2016-01-01

, inoffensive and inexpensive 3D scanning modality based on structured light, suitable for capturing the morphology and the appearance of specimens. Benefits of having 3D models are manifold. The 3D models are easy to share among researchers and can be made available to the general public. Advanced...... morphological modelling is possible with accurate description of the specimens provided by the models. Furthermore, performing studies on models reduces the risk of damage to the original specimen. In our work we employ a high resolution structured light scanner for digitalizing a collection of 8500 year old...... human skulls from Brazil. To evaluate the precision of our setup we compare the structured light scan to micro-CT and achieve submillimetre difference. We analyse morphological features of the Brazilian skulls using manual landmarks, but a research goal is to automate this, fully utilize the dense 3D...

Development of a 3D bone marrow adipose tissue model.

Science.gov (United States)

Fairfield, Heather; Falank, Carolyne; Farrell, Mariah; Vary, Calvin; Boucher, Joshua M; Driscoll, Heather; Liaw, Lucy; Rosen, Clifford J; Reagan, Michaela R

2018-01-26

Over the past twenty years, evidence has accumulated that biochemically and spatially defined networks of extracellular matrix, cellular components, and interactions dictate cellular differentiation, proliferation, and function in a variety of tissue and diseases. Modeling in vivo systems in vitro has been undeniably necessary, but when simplified 2D conditions rather than 3D in vitro models are used, the reliability and usefulness of the data derived from these models decreases. Thus, there is a pressing need to develop and validate reliable in vitro models to reproduce specific tissue-like structures and mimic functions and responses of cells in a more realistic manner for both drug screening/disease modeling and tissue regeneration applications. In adipose biology and cancer research, these models serve as physiologically relevant 3D platforms to bridge the divide between 2D cultures and in vivo models, bringing about more reliable and translationally useful data to accelerate benchtop to bedside research. Currently, no model has been developed for bone marrow adipose tissue (BMAT), a novel adipose depot that has previously been overlooked as "filler tissue" but has more recently been recognized as endocrine-signaling and systemically relevant. Herein we describe the development of the first 3D, BMAT model derived from either human or mouse bone marrow (BM) mesenchymal stromal cells (MSCs). We found that BMAT models can be stably cultured for at least 3 months in vitro, and that myeloma cells (5TGM1, OPM2 and MM1S cells) can be cultured on these for at least 2 weeks. Upon tumor cell co-culture, delipidation occurred in BMAT adipocytes, suggesting a bidirectional relationship between these two important cell types in the malignant BM niche. Overall, our studies suggest that 3D BMAT represents a "healthier," more realistic tissue model that may be useful for elucidating the effects of MAT on tumor cells, and tumor cells on MAT, to identify novel therapeutic

A Hybrid 3D Indoor Space Model

Directory of Open Access Journals (Sweden)

A. Jamali

2016-10-01

Full Text Available GIS integrates spatial information and spatial analysis. An important example of such integration is for emergency response which requires route planning inside and outside of a building. Route planning requires detailed information related to indoor and outdoor environment. Indoor navigation network models including Geometric Network Model (GNM, Navigable Space Model, sub-division model and regular-grid model lack indoor data sources and abstraction methods. In this paper, a hybrid indoor space model is proposed. In the proposed method, 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. This research proposes a method of indoor space modeling for the buildings which do not have proper 2D/3D geometrical models or they lack semantic or topological information. The proposed hybrid model consists of topological, geometrical and semantical space.

BEAMS3D Neutral Beam Injection Model

Energy Technology Data Exchange (ETDEWEB)

Lazerson, Samuel

2014-04-14

With the advent of applied 3D fi elds in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous velocity reduction, and pitch angle scattering are modeled with the ADAS atomic physics database [1]. Benchmark calculations are presented to validate the collisionless particle orbits, neutral beam injection model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields.

Streamlining the Process of 3D Printing a Brain From a Structural MRI

Directory of Open Access Journals (Sweden)

Daniel Peterson

2017-05-01

Full Text Available Currently, the process of obtaining a 3D model from a structural MRI requires specialized knowlege and skills. This is not due to the fundamental difficulty and complexity of the process, but is a result of the fact that the neccessary tools were developed for and by neuroimaging researchers. This project describes a publically available utility implemented as a Docker image that takes a structural MRI as input, and gives files for 3D printing as output, along with a rendered image of the surface.

Large-scale 3-D modeling by integration of resistivity models and borehole data through inversion

DEFF Research Database (Denmark)

Foged, N.; Marker, Pernille Aabye; Christiansen, A. V.

2014-01-01

resistivity and the clay fraction. Through inversion we use the lithological data and the resistivity data to determine the optimum spatially distributed translator function. Applying the translator function we get a 3-D clay fraction model, which holds information from the resistivity data set...... and the borehole data set in one variable. Finally, we use k-means clustering to generate a 3-D model of the subsurface structures. We apply the procedure to the Norsminde survey in Denmark, integrating approximately 700 boreholes and more than 100 000 resistivity models from an airborne survey...

The crystal structure of γ-AlD3

International Nuclear Information System (INIS)

Brinks, H.W.; Brown, C.; Jensen, C.M.; Graetz, J.; Reilly, J.J.; Hauback, B.C.

2007-01-01

γ-AlD 3 was synthesized from LiAlD 4 and AlCl 3 via thermal decomposition of aluminum hydride etherate in presence of excess LiAlD 4 . γ-AlD 3 was determined by powder neutron diffraction and synchrotron X-ray diffraction to crystallize in the space group Pnnm. The orthorhombic structure has unit-cell dimensions a = 7.3360(3) A, b = 5.3672(2) A and c = 5.7562(1) A, and it consists of both corner- and edge-sharing AlD 6 octahedra where each hydrogen is shared between two octahedra. The average Al-D distances in octahedra with edge-sharing is 1.706 A and in the octahedra with only corner-sharing 1.719 A

Low-cost structured-light based 3D capture system design

Science.gov (United States)

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.

Image based 3D city modeling : Comparative study

Directory of Open Access Journals (Sweden)

S. P. Singh

2014-06-01

Full Text Available 3D city model is a digital representation of the Earth’s surface and it’s related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing rapidly for various engineering and non-engineering applications. Generally four main image based approaches were used for virtual 3D city models generation. In first approach, researchers were used Sketch based modeling, second method is Procedural grammar based modeling, third approach is Close range photogrammetry based modeling and fourth approach is mainly based on Computer Vision techniques. SketchUp, CityEngine, Photomodeler and Agisoft Photoscan are the main softwares to represent these approaches respectively. These softwares have different approaches & methods suitable for image based 3D city modeling. Literature study shows that till date, there is no complete such type of comparative study available to create complete 3D city model by using images. This paper gives a comparative assessment of these four image based 3D modeling approaches. This comparative study is mainly based on data acquisition methods, data processing techniques and output 3D model products. For this research work, study area is the campus of civil engineering department, Indian Institute of Technology, Roorkee (India. This 3D campus acts as a prototype for city. This study also explains various governing parameters, factors and work experiences. This research work also gives a brief introduction, strengths and weakness of these four image based techniques. Some personal comment is also given as what can do or what can’t do from these softwares. At the last, this study shows; it concluded that, each and every software has some advantages and limitations. Choice of software depends on user requirements of 3D project. For normal visualization project, SketchUp software is a good option. For 3D documentation record, Photomodeler gives good

Complete Tem-Tomography: 3D Structure of Gems Cluster

Science.gov (United States)

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.

A 3D Printing Model Watermarking Algorithm Based on 3D Slicing and Feature Points

Directory of Open Access Journals (Sweden)

Giao N. Pham

2018-02-01

Full Text Available With the increase of three-dimensional (3D printing applications in many areas of life, a large amount of 3D printing data is copied, shared, and used several times without any permission from the original providers. Therefore, copyright protection and ownership identification for 3D printing data in communications or commercial transactions are practical issues. This paper presents a novel watermarking algorithm for 3D printing models based on embedding watermark data into the feature points of a 3D printing model. Feature points are determined and computed by the 3D slicing process along the Z axis of a 3D printing model. The watermark data is embedded into a feature point of a 3D printing model by changing the vector length of the feature point in OXY space based on the reference length. The x and y coordinates of the feature point will be then changed according to the changed vector length that has been embedded with a watermark. Experimental results verified that the proposed algorithm is invisible and robust to geometric attacks, such as rotation, scaling, and translation. The proposed algorithm provides a better method than the conventional works, and the accuracy of the proposed algorithm is much higher than previous methods.

Finding the displacement of wood structure in heritage building by 3D laser scanner

Science.gov (United States)

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.

Structure of d-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate d-3-hydroxybutyrate and NAD+

International Nuclear Information System (INIS)

Hoque, Md Mominul; Shimizu, Satoru; Juan, Ella Czarina Magat; Sato, Yoshiteru; Hossain, Md Tofazzal; Yamamoto, Tamotsu; Imamura, Shigeyuki; Suzuki, Kaoru; Amano, Hitoshi; Sekiguchi, Takeshi; Tsunoda, Masaru; Takénaka, Akio

2009-01-01

The crystal structure of A. faecalisd-3-hydroxybutyrate dehydrogenase prepared in the presence of d-3-hydroxybutyrate and NAD + reveals the substrate/product-binding geometry as the first example which suggests that the catalytic reaction occurs by shuttle movements of a hydrogen negative ion from the substrate to NAD + and from NADH to the product. d-3-Hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between d-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate d-3-hydroxybutyrate and the cofactor NAD + at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD + and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of d-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure

2.5D real waveform and real noise simulation of receiver functions in 3D models

Science.gov (United States)

Schiffer, Christian; Jacobsen, Bo; Balling, Niels

2014-05-01

, the comparison can even be made quantitative, and an iterative inverse 3D model updating would be possible. Furthermore the "2.5D" modelling approach of the in reality 3D problem must be investigated in terms of accuracy of the approximation, in particular with focus on highly 3D structures and multiple phases. References: Schiffer et al. 2013, A fossil subduction zone in the East Greenland Caledonides revealed by a Receiver Function analysis, Geophysical Research Abstracts, Vol. 15, EGU2013-6947, 2013, EGU General Assembly 2013 Schlindwein, V. and Jokat, W., 1999, Structure and evolution of the continental crust of northern east Greenland from integrated geophysical studies: Journal of Geophysical Research, v. 104, no. B7, p. 15227-15,245 Voss, M. and Jokat, W., 2007, Continent-ocean transition and voluminous magmatic underplating derived from P-wave velocity modelling of the East Greenland continental margin: Geophysical Journal International, v.170, no. 2, p. 580-604

From 2D to 3D: Using Illumination Cones to Build 3d Face Model

International Nuclear Information System (INIS)

Xiao, S S; Jin, M

2006-01-01

To solve the problem derivate by lighting condition and position of the camera, a new method using illumination cones to build 3d face model has been proposed. Due to illumination variability, the same object can show dramatic difference even as being viewed in fixed pose. To handle this variability, an object recognition system must employ a representation that is either invariant to, or can model this variability. The proposed technique presents an appearance-based method for modeling the variability due to illumination in the images of objects. The method differs from past appearance-based methods. Evenmore, a small set of training images is used to generate a representation that the illumination cone models the complete set of images of an object with Lambertian reflectance surface under a combination of arbitrary point light sources at infinity. After building up the illumination cones, researches focus on how to present the 3d model of the face. Combining illumination and texture feature to build up 3d model of the face make it easy solving the problem in recognition of face under different pose

Topology optimization of 3D shell structures with porous infill

DEFF Research Database (Denmark)

Clausen, Anders; Andreassen, Erik; Sigmund, Ole

2017-01-01

This paper presents a 3D topology optimization approach for designing shell structures with a porous or void interior. It is shown that the resulting structures are significantly more robust towards load perturbations than completely solid structures optimized under the same conditions. The study...... indicates that the potential benefit of using porous structures is higher for lower total volume fractions. Compared to earlier work dealing with 2D topology optimization, we found several new effects in 3D problems. Most notably, the opportunity for designing closed shells significantly improves...

Development and characterization of a 3D multicell microtissue culture model of airway smooth muscle.

Science.gov (United States)

West, Adrian R; Zaman, Nishat; Cole, Darren J; Walker, Matthew J; Legant, Wesley R; Boudou, Thomas; Chen, Christopher S; Favreau, John T; Gaudette, Glenn R; Cowley, Elizabeth A; Maksym, Geoffrey N

2013-01-01

Airway smooth muscle (ASM) cellular and molecular biology is typically studied with single-cell cultures grown on flat 2D substrates. However, cells in vivo exist as part of complex 3D structures, and it is well established in other cell types that altering substrate geometry exerts potent effects on phenotype and function. These factors may be especially relevant to asthma, a disease characterized by structural remodeling of the airway wall, and highlights a need for more physiologically relevant models of ASM function. We utilized a tissue engineering platform known as microfabricated tissue gauges to develop a 3D culture model of ASM featuring arrays of ∼0.4 mm long, ∼350 cell "microtissues" capable of simultaneous contractile force measurement and cell-level microscopy. ASM-only microtissues generated baseline tension, exhibited strong cellular organization, and developed actin stress fibers, but lost structural integrity and dissociated from the cantilevers within 3 days. Addition of 3T3-fibroblasts dramatically improved survival times without affecting tension development or morphology. ASM-3T3 microtissues contracted similarly to ex vivo ASM, exhibiting reproducible responses to a range of contractile and relaxant agents. Compared with 2D cultures, microtissues demonstrated identical responses to acetylcholine and KCl, but not histamine, forskolin, or cytochalasin D, suggesting that contractility is regulated by substrate geometry. Microtissues represent a novel model for studying ASM, incorporating a physiological 3D structure, realistic mechanical environment, coculture of multiple cells types, and comparable contractile properties to existing models. This new model allows for rapid screening of biochemical and mechanical factors to provide insight into ASM dysfunction in asthma.

Combining Synchronous and Asynchronous Collaboration within 3D City Models

Science.gov (United States)

Klimke, Jan; Döllner, Jürgen

This paper presents an approach for combining spatially distributed synchronous and asynchronous collaboration within 3D city models. Software applications use these models as additional communication medium to facilitate communication of georeferenced and geospatial information. Collaboration tools should support both the communication with other collaborators and their awareness of the current collaboration context. To support collaborative knowledge construction and gathering, we have designed a collaboration system to facilitate (a) creation of annotations that have 3D references to the virtual 3D city model and (b) collection information about the context in which these annotations are created. Our approach supports synchronous collaboration in connection with the creation of non volatile, precisely georeferenced units of information allow for a comprehensible form of cooperation in spatially distributed settings. Storage and retrieval of this information is provided through a Web Feature Service, which eases integration of collaboration data into existing applications. We further introduce a visualization technique that integrates annotations as complex structured data into the 3D visualization. This avoids media breaks and disruptions in working processes and creates a spatial coherence between annotation and annotated feature or geometry.

3D MODELLING BY LOW-COST RANGE CAMERA: SOFTWARE EVALUATION AND COMPARISON

Directory of Open Access Journals (Sweden)

R. Ravanelli

2017-11-01

Full Text Available The aim of this work is to present a comparison among three software applications currently available for the Occipital Structure SensorTM; all these software were developed for collecting 3D models of objects easily and in real-time with this structured light range camera. The SKANECT, itSeez3D and Scanner applications were thus tested: a DUPLOTM bricks construction was scanned with the three applications and the obtained models were compared to the model virtually generated with a standard CAD software, which served as reference. The results demonstrate that all the software applications are generally characterized by the same level of geometric accuracy, which amounts to very few millimetres. However, the itSeez3D software, which requires a payment of $7 to export each model, represents surely the best solution, both from the point of view of the geometric accuracy and, mostly, at the level of the color restitution. On the other hand, Scanner, which is a free software, presents an accuracy comparable to that of itSeez3D. At the same time, though, the colors are often smoothed and not perfectly overlapped to the corresponding part of the model. Lastly, SKANECT is the software that generates the highest number of points, but it has also some issues with the rendering of the colors.

Modeling of 3d Space-time Surface of Potential Fields and Hydrogeologic Modeling of Nuclear Waste Disposal Sites

Science.gov (United States)

Shestopalov, V.; Bondarenko, Y.; Zayonts, I.; Rudenko, Y.

extracted from the total vertical and hori- zontal gradient respectively, both shaded from the 5 northeast to 355 northwest. The dip of multi-layer surfaces indicates the down -"gradient" direction in the fields. The methodology of 3D STSI is based on the analysis of vertical and horizontal anisotropy of gravity and magnetic fields, as well as of multi-layer 3D space-time surface model (3D STSM) of the stress fields. The 3D STSM is multi-layer topology structure of 1 lineaments or gradients (edges) and surfaces calculated by uniform matrices of the geophysical fields. One of the information components of the stress fields character- istics is the aspects and slopes for compressive and tensile stresses. Overlaying of the 3D STSI and lineaments with maps of multi-layer gradients enables to create highly reliable 3D Space-Time Kinematic Model "3D STKM". The analysis of 3D STKM in- cluded: - the space-time reconstruct of forces direction and strain distribution scheme during formation of geological structures and structural paragenesis (lineaments) of potential fields; - predict the real location of expected tectonic dislocations, zones of rock fracturing and disintegration, and mass-stable blocks. Based on these data, the 3D STSM are drawn which reflect the geodynamics of territory development on the ground of paleotectonic reconstruction of successive activity stages having formed the present-day lithosphere. Thus three-dimensional STSM allows to construct an un- mixing geodynamic processes in any interval of fixed space-time in coordinates x, y, t(z). The integrated of the 3D STSM and 3D seismic models enables also to create structural-kinematic and geodynamic maps of the Earth's crust at different depth. As a result, the classification of CNPP areas is performed into zones of compressive and tensile stresses characterized by enhanced permeability of rocks, and zones of consoli- dation with minimal rocks permeability. In addition, the vertically alternating zones of

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

Science.gov (United States)

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

2016-04-20

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

Embedded sensing: integrating sensors in 3-D printed structures

Directory of Open Access Journals (Sweden)

A. Dijkshoorn

2018-03-01

Full Text Available Current additive manufacturing allows for the implementation of electrically interrogated 3-D printed sensors. In this contribution various technologies, sensing principles and applications are discussed. We will give both an overview of some of the sensors presented in literature as well as some of our own recent work on 3-D printed sensors. The 3-D printing methods discussed include fused deposition modelling (FDM, using multi-material printing and poly-jetting. Materials discussed are mainly thermoplastics and include thermoplastic polyurethane (TPU, both un-doped as well as doped with carbon black, polylactic acid (PLA and conductive inks. The sensors discussed are based on biopotential sensing, capacitive sensing and resistive sensing with applications in surface electromyography (sEMG and mechanical and tactile sensing. As these sensors are based on plastics they are in general flexible and therefore open new possibilities for sensing in soft structures, e.g. as used in soft robotics. At the same time they show many of the characteristics of plastics like hysteresis, drift and non-linearity. We will argue that 3-D printing of embedded sensors opens up exciting new possibilities but also that these sensors require us to rethink how to exploit non-ideal sensors.

I-TASSER server for protein 3D structure prediction

Directory of Open Access Journals (Sweden)

Zhang Yang

2008-01-01

Full Text Available Abstract Background Prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. The community-wide Critical Assessment of Structure Prediction (CASP experiments have been designed to obtain an objective assessment of the state-of-the-art of the field, where I-TASSER was ranked as the best method in the server section of the recent 7th CASP experiment. Our laboratory has since then received numerous requests about the public availability of the I-TASSER algorithm and the usage of the I-TASSER predictions. Results An on-line version of I-TASSER is developed at the KU Center for Bioinformatics which has generated protein structure predictions for thousands of modeling requests from more than 35 countries. A scoring function (C-score based on the relative clustering structural density and the consensus significance score of multiple threading templates is introduced to estimate the accuracy of the I-TASSER predictions. A large-scale benchmark test demonstrates a strong correlation between the C-score and the TM-score (a structural similarity measurement with values in [0, 1] of the first models with a correlation coefficient of 0.91. Using a C-score cutoff > -1.5 for the models of correct topology, both false positive and false negative rates are below 0.1. Combining C-score and protein length, the accuracy of the I-TASSER models can be predicted with an average error of 0.08 for TM-score and 2 Å for RMSD. Conclusion The I-TASSER server has been developed to generate automated full-length 3D protein structural predictions where the benchmarked scoring system helps users to obtain quantitative assessments of the I-TASSER models. The output of the I-TASSER server for each query includes up to five full-length models, the confidence score, the estimated TM-score and RMSD, and the standard deviation of the estimations. The I-TASSER server is freely available

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

DEFF Research Database (Denmark)

Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2013-01-01

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...... 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 22495 3D modules in all PDB files results in 977 internal loop...

Creation of 3D Multi-Body Orthodontic Models by Using Independent Imaging Sensors

Directory of Open Access Journals (Sweden)

Armando Viviano Razionale

2013-02-01

Full Text Available In the field of dental health care, plaster models combined with 2D radiographs are widely used in clinical practice for orthodontic diagnoses. However, complex malocclusions can be better analyzed by exploiting 3D digital dental models, which allow virtual simulations and treatment planning processes. In this paper, dental data captured by independent imaging sensors are fused to create multi-body orthodontic models composed of teeth, oral soft tissues and alveolar bone structures. The methodology is based on integrating Cone-Beam Computed Tomography (CBCT and surface structured light scanning. The optical scanner is used to reconstruct tooth crowns and soft tissues (visible surfaces through the digitalization of both patients’ mouth impressions and plaster casts. These data are also used to guide the segmentation of internal dental tissues by processing CBCT data sets. The 3D individual dental tissues obtained by the optical scanner and the CBCT sensor are fused within multi-body orthodontic models without human supervisions to identify target anatomical structures. The final multi-body models represent valuable virtual platforms to clinical diagnostic and treatment planning.

Crustal metamorphic fluid flux beneath the Dead Sea Basin: constraints from 2-D and 3-D magnetotelluric modelling

Science.gov (United States)

Meqbel, Naser; Weckmann, Ute; Muñoz, Gerard; Ritter, Oliver

2016-12-01

We report on a study to explore the deep electrical conductivity structure of the Dead Sea Basin (DSB) using magnetotelluric (MT) data collected along a transect across the DSB where the left lateral strike-slip Dead Sea transform (DST) fault splits into two fault strands forming one of the largest pull-apart basins of the world. A very pronounced feature of our 2-D inversion model is a deep, subvertical conductive zone beneath the DSB. The conductor extends through the entire crust and is sandwiched between highly resistive structures associated with Precambrian rocks of the basin flanks. The high electrical conductivity could be attributed to fluids released by dehydration of the uppermost mantle beneath the DSB, possibly in combination with fluids released by mid- to low-grade metamorphism in the lower crust and generation of hydrous minerals in the middle crust through retrograde metamorphism. Similar high conductivity zones associated with fluids have been reported from other large fault systems. The presence of fluids and hydrous minerals in the middle and lower crust could explain the required low friction coefficient of the DST along the eastern boundary of the DSB and the high subsidence rate of basin sediments. 3-D inversion models confirm the existence of a subvertical high conductivity structure underneath the DSB but its expression is far less pronounced. Instead, the 3-D inversion model suggests a deepening of the conductive DSB sediments off-profile towards the south, reaching a maximum depth of approximately 12 km, which is consistent with other geophysical observations. At shallower levels, the 3-D inversion model reveals salt diapirism as an upwelling of highly resistive structures, localized underneath the Al-Lisan Peninsula. The 3-D model furthermore contains an E-W elongated conductive structure to the northeast of the DSB. More MT data with better spatial coverage are required, however, to fully constrain the robustness of the above

Finite-Source Inversion for the 2004 Parkfield Earthquake using 3D Velocity Model Green's Functions

Science.gov (United States)

Kim, A.; Dreger, D.; Larsen, S.

2008-12-01

We determine finite fault models of the 2004 Parkfield earthquake using 3D Green's functions. Because of the dense station coverage and detailed 3D velocity structure model in this region, this earthquake provides an excellent opportunity to examine how the 3D velocity structure affects the finite fault inverse solutions. Various studies (e.g. Michaels and Eberhart-Phillips, 1991; Thurber et al., 2006) indicate that there is a pronounced velocity contrast across the San Andreas Fault along the Parkfield segment. Also the fault zone at Parkfield is wide as evidenced by mapped surface faults and where surface slip and creep occurred in the 1966 and the 2004 Parkfield earthquakes. For high resolution images of the rupture process"Ait is necessary to include the accurate 3D velocity structure for the finite source inversion. Liu and Aurchuleta (2004) performed finite fault inversions using both 1D and 3D Green's functions for 1989 Loma Prieta earthquake using the same source paramerization and data but different Green's functions and found that the models were quite different. This indicates that the choice of the velocity model significantly affects the waveform modeling at near-fault stations. In this study, we used the P-wave velocity model developed by Thurber et al (2006) to construct the 3D Green's functions. P-wave speeds are converted to S-wave speeds and density using by the empirical relationships of Brocher (2005). Using a finite difference method, E3D (Larsen and Schultz, 1995), we computed the 3D Green's functions numerically by inserting body forces at each station. Using reciprocity, these Green's functions are recombined to represent the ground motion at each station due to the slip on the fault plane. First we modeled the waveforms of small earthquakes to validate the 3D velocity model and the reciprocity of the Green"fs function. In the numerical tests we found that the 3D velocity model predicted the individual phases well at frequencies lower than 0

A 3D gravity and magnetic model for the Entenschnabel area (German North Sea)

Science.gov (United States)

Dressel, Ingo; Barckhausen, Udo; Heyde, Ingo

2018-01-01

In this study, we focus on structural configuration of the Entenschnabel area, a part of the German exclusive economic zone within the North Sea, by means of gravity and magnetic modelling. The starting point of the 3D modelling approach is published information on subseafloor structures for shallow depths, acquired by wells and seismic surveys. Subsequent gravity and magnetic modelling of the structures of the deeper subsurface builds on this geophysical and geological information and on gravity and magnetic data acquired during a research cruise to the Entenschnabel area. On the one hand, our 3D model shows the density and susceptibility distribution of the sediments and the crust. In addition, the potential field modelling provides evidence for a differentiation between lower and upper crust. The thickness distribution of the crust is also discussed with respect to the tectonic framework. Furthermore, gravity as well as magnetic modelling points to an intrusive complex beneath the Central Graben within the Entenschnabel area. On the other hand, this work provides a geological-geophysical consistent 3D gravity and magnetic model that can be used as a starting point for further investigation of this part of the German North Sea.

Evaluation of 3D Printer Accuracy in Producing Fractal Structure.

Science.gov (United States)

Kikegawa, Kana; Takamatsu, Kyuuichirou; Kawakami, Masaru; Furukawa, Hidemitsu; Mayama, Hiroyuki; Nonomura, Yoshimune

2017-01-01

Hierarchical structures, also known as fractal structures, exhibit advantageous material properties, such as water- and oil-repellency as well as other useful optical characteristics, owing to its self-similarity. Various methods have been developed for producing hierarchical geometrical structures. Recently, fractal structures have been manufactured using a 3D printing technique that involves computer-aided design data. In this study, we confirmed the accuracy of geometrical structures when Koch curve-like fractal structures with zero to three generations were printed using a 3D printer. The fractal dimension was analyzed using a box-counting method. This analysis indicated that the fractal dimension of the third generation hierarchical structure was approximately the same as that of the ideal Koch curve. These findings demonstrate that the design and production of fractal structures can be controlled using a 3D printer. Although the interior angle deviated from the ideal value, the side length could be precisely controlled.

Potential of 3D City Models to assess flood vulnerability

Science.gov (United States)

Schröter, Kai; Bochow, Mathias; Schüttig, Martin; Nagel, Claus; Ross, Lutz; Kreibich, Heidi

2016-04-01

Vulnerability, as the product of exposure and susceptibility, is a key factor of the flood risk equation. Furthermore, the estimation of flood loss is very sensitive to the choice of the vulnerability model. Still, in contrast to elaborate hazard simulations, vulnerability is often considered in a simplified manner concerning the spatial resolution and geo-location of exposed objects as well as the susceptibility of these objects at risk. Usually, area specific potential flood loss is quantified on the level of aggregated land-use classes, and both hazard intensity and resistance characteristics of affected objects are represented in highly simplified terms. We investigate the potential of 3D City Models and spatial features derived from remote sensing data to improve the differentiation of vulnerability in flood risk assessment. 3D City Models are based on CityGML, an application scheme of the Geography Markup Language (GML), which represents the 3D geometry, 3D topology, semantics and appearance of objects on different levels of detail. As such, 3D City Models offer detailed spatial information which is useful to describe the exposure and to characterize the susceptibility of residential buildings at risk. This information is further consolidated with spatial features of the building stock derived from remote sensing data. Using this database a spatially detailed flood vulnerability model is developed by means of data-mining. Empirical flood damage data are used to derive and to validate flood susceptibility models for individual objects. We present first results from a prototype application in the city of Dresden, Germany. The vulnerability modeling based on 3D City Models and remote sensing data is compared i) to the generally accepted good engineering practice based on area specific loss potential and ii) to a highly detailed representation of flood vulnerability based on a building typology using urban structure types. Comparisons are drawn in terms of

3D Modeling Techniques for Print and Digital Media

Science.gov (United States)

Stephens, Megan Ashley

In developing my thesis, I looked to gain skills using ZBrush to create 3D models, 3D scanning, and 3D printing. The models created compared the hearts of several vertebrates and were intended for students attending Comparative Vertebrate Anatomy. I used several resources to create a model of the human heart and was able to work from life while creating heart models from other vertebrates. I successfully learned ZBrush and 3D scanning, and successfully printed 3D heart models. ZBrush allowed me to create several intricate models for use in both animation and print media. The 3D scanning technique did not fit my needs for the project, but may be of use for later projects. I was able to 3D print using two different techniques as well.

Automated 3D Damaged Cavity Model Builder for Lower Surface Acreage Tile on Orbiter

Science.gov (United States)

Belknap, Shannon; Zhang, Michael

2013-01-01

The 3D Automated Thermal Tool for Damaged Acreage Tile Math Model builder was developed to perform quickly and accurately 3D thermal analyses on damaged lower surface acreage tiles and structures beneath the damaged locations on a Space Shuttle Orbiter. The 3D model builder created both TRASYS geometric math models (GMMs) and SINDA thermal math models (TMMs) to simulate an idealized damaged cavity in the damaged tile(s). The GMMs are processed in TRASYS to generate radiation conductors between the surfaces in the cavity. The radiation conductors are inserted into the TMMs, which are processed in SINDA to generate temperature histories for all of the nodes on each layer of the TMM. The invention allows a thermal analyst to create quickly and accurately a 3D model of a damaged lower surface tile on the orbiter. The 3D model builder can generate a GMM and the correspond ing TMM in one or two minutes, with the damaged cavity included in the tile material. A separate program creates a configuration file, which would take a couple of minutes to edit. This configuration file is read by the model builder program to determine the location of the damage, the correct tile type, tile thickness, structure thickness, and SIP thickness of the damage, so that the model builder program can build an accurate model at the specified location. Once the models are built, they are processed by the TRASYS and SINDA.

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

Science.gov (United States)

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

2016-06-15

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

International Nuclear Information System (INIS)

Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

2016-01-01

We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

KAUST Repository

Wang, Cheng

2018-01-01

Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome

AUTOMATIC MESH GENERATION OF 3-D GEOMETRIC MODELS

Institute of Scientific and Technical Information of China (English)

刘剑飞

2003-01-01

In this paper the presentation of the ball-packing method is reviewed,and a scheme to generate mesh for complex 3-D geometric models is given,which consists of 4 steps:(1)create nodes in 3-D models by ball-packing method,(2)connect nodes to generate mesh by 3-D Delaunay triangulation,(3)retrieve the boundary of the model after Delaunay triangulation,(4)improve the mesh.

Comparison of 3D Echocardiogram-Derived 3D Printed Valve Models to Molded Models for Simulated Repair of Pediatric Atrioventricular Valves.

Science.gov (United States)

Scanlan, Adam B; Nguyen, Alex V; Ilina, Anna; Lasso, Andras; Cripe, Linnea; Jegatheeswaran, Anusha; Silvestro, Elizabeth; McGowan, Francis X; Mascio, Christopher E; Fuller, Stephanie; Spray, Thomas L; Cohen, Meryl S; Fichtinger, Gabor; Jolley, Matthew A

2018-03-01

Mastering the technical skills required to perform pediatric cardiac valve surgery is challenging in part due to limited opportunity for practice. Transformation of 3D echocardiographic (echo) images of congenitally abnormal heart valves to realistic physical models could allow patient-specific simulation of surgical valve repair. We compared materials, processes, and costs for 3D printing and molding of patient-specific models for visualization and surgical simulation of congenitally abnormal heart valves. Pediatric atrioventricular valves (mitral, tricuspid, and common atrioventricular valve) were modeled from transthoracic 3D echo images using semi-automated methods implemented as custom modules in 3D Slicer. Valve models were then both 3D printed in soft materials and molded in silicone using 3D printed "negative" molds. Using pre-defined assessment criteria, valve models were evaluated by congenital cardiac surgeons to determine suitability for simulation. Surgeon assessment indicated that the molded valves had superior material properties for the purposes of simulation compared to directly printed valves (p 3D echo-derived molded valves are a step toward realistic simulation of complex valve repairs but require more time and labor to create than directly printed models. Patient-specific simulation of valve repair in children using such models may be useful for surgical training and simulation of complex congenital cases.

Fiducial-based fusion of 3D dental models with magnetic resonance imaging.

Science.gov (United States)

Abdi, Amir H; Hannam, Alan G; Fels, Sidney

2018-04-16

Magnetic resonance imaging (MRI) is widely used in study of maxillofacial structures. While MRI is the modality of choice for soft tissues, it fails to capture hard tissues such as bone and teeth. Virtual dental models, acquired by optical 3D scanners, are becoming more accessible for dental practice and are starting to replace the conventional dental impressions. The goal of this research is to fuse the high-resolution 3D dental models with MRI to enhance the value of imaging for applications where detailed analysis of maxillofacial structures are needed such as patient examination, surgical planning, and modeling. A subject-specific dental attachment was digitally designed and 3D printed based on the subject's face width and dental anatomy. The attachment contained 19 semi-ellipsoidal concavities in predetermined positions where oil-based ellipsoidal fiducial markers were later placed. The MRI was acquired while the subject bit on the dental attachment. The spatial position of the center of mass of each fiducial in the resultant MR Image was calculated by averaging its voxels' spatial coordinates. The rigid transformation to fuse dental models to MRI was calculated based on the least squares mapping of corresponding fiducials and solved via singular-value decomposition. The target registration error (TRE) of the proposed fusion process, calculated in a leave-one-fiducial-out fashion, was estimated at 0.49 mm. The results suggest that 6-9 fiducials suffice to achieve a TRE of equal to half the MRI voxel size. Ellipsoidal oil-based fiducials produce distinguishable intensities in MRI and can be used as registration fiducials. The achieved accuracy of the proposed approach is sufficient to leverage the merged 3D dental models with the MRI data for a finer analysis of the maxillofacial structures where complete geometry models are needed.

Reassessing Geophysical Models of the Bushveld Complex in 3D

Science.gov (United States)

Cole, J.; Webb, S. J.; Finn, C.

2012-12-01

Conceptual geophysical models of the Bushveld Igneous Complex show three possible geometries for its mafic component: 1) Separate intrusions with vertical feeders for the eastern and western lobes (Cousins, 1959) 2) Separate dipping sheets for the two lobes (Du Plessis and Kleywegt, 1987) 3) A single saucer-shaped unit connected at depth in the central part between the two lobes (Cawthorn et al, 1998) Model three incorporates isostatic adjustment of the crust in response to the weight of the dense mafic material. The model was corroborated by results of a broadband seismic array over southern Africa, known as the Southern African Seismic Experiment (SASE) (Nguuri, et al, 2001; Webb et al, 2004). This new information about the crustal thickness only became available in the last decade and could not be considered in the earlier models. Nevertheless, there is still on-going debate as to which model is correct. All of the models published up to now have been done in 2 or 2.5 dimensions. This is not well suited to modelling the complex geometry of the Bushveld intrusion. 3D modelling takes into account effects of variations in geometry and geophysical properties of lithologies in a full three dimensional sense and therefore affects the shape and amplitude of calculated fields. The main question is how the new knowledge of the increased crustal thickness, as well as the complexity of the Bushveld Complex, will impact on the gravity fields calculated for the existing conceptual models, when modelling in 3D. The three published geophysical models were remodelled using full 3Dl potential field modelling software, and including crustal thickness obtained from the SASE. The aim was not to construct very detailed models, but to test the existing conceptual models in an equally conceptual way. Firstly a specific 2D model was recreated in 3D, without crustal thickening, to establish the difference between 2D and 3D results. Then the thicker crust was added. Including the less

A novel knowledge-based potential for RNA 3D structure evaluation

Science.gov (United States)

Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

2018-03-01

Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).

p3d – Python module for structural bioinformatics

Directory of Open Access Journals (Sweden)

Fufezan Christian

2009-08-01

Full Text Available Abstract Background High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. Results p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files. p3d's strength arises from the combination of a very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP tree, b set theory and c functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

3D reconstruction of internal structure of animal body using near-infrared light

Science.gov (United States)

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.

Illustrating the disassembly of 3D models

KAUST Repository

Guo, Jianwei; Yan, Dongming; Li, Er; Dong, Weiming; Wonka, Peter; Zhang, Xiaopeng

2013-01-01

We present a framework for the automatic disassembly of 3D man-made models and the illustration of the disassembly process. Given an assembled 3D model, we first analyze the individual parts using sharp edge loops and extract the contact faces

Automatic Generation of Structural Building Descriptions from 3D Point Cloud Scans

DEFF Research Database (Denmark)

Ochmann, Sebastian; Vock, Richard; Wessel, Raoul

2013-01-01

We present a new method for automatic semantic structuring of 3D point clouds representing buildings. In contrast to existing approaches which either target the outside appearance like the facade structure or rather low-level geometric structures, we focus on the building’s interior using indoor...... scans to derive high-level architectural entities like rooms and doors. Starting with a registered 3D point cloud, we probabilistically model the affiliation of each measured point to a certain room in the building. We solve the resulting clustering problem using an iterative algorithm that relies...... on the estimated visibilities between any two locations within the point cloud. With the segmentation into rooms at hand, we subsequently determine the locations and extents of doors between adjacent rooms. In our experiments, we demonstrate the feasibility of our method by applying it to synthetic as well...

3D physical modeling for patterning process development

Science.gov (United States)

Sarma, Chandra; Abdo, Amr; Bailey, Todd; Conley, Will; Dunn, Derren; Marokkey, Sajan; Talbi, Mohamed

2010-03-01

In this paper we will demonstrate how a 3D physical patterning model can act as a forensic tool for OPC and ground-rule development. We discuss examples where the 2D modeling shows no issues in printing gate lines but 3D modeling shows severe resist loss in the middle. In absence of corrective measure, there is a high likelihood of line discontinuity post etch. Such early insight into process limitations of prospective ground rules can be invaluable for early technology development. We will also demonstrate how the root cause of broken poly-line after etch could be traced to resist necking in the region of STI step with the help of 3D models. We discuss different cases of metal and contact layouts where 3D modeling gives an early insight in to technology limitations. In addition such a 3D physical model could be used for early resist evaluation and selection for required ground-rule challenges, which can substantially reduce the cycle time for process development.

Reactive flow simulation in complex 3D geometries using the COM3D code

International Nuclear Information System (INIS)

Breitung, W.; Kotchourko, A.; Veser, A.; Scholtyssek, W.

1999-01-01

The COM3D code, under development at the Forschungszentrum Karlsruhe (FZK), is a 3-d CFD code to describe turbulent combustion phenomena in complex geometries. It is intended to be part of the advanced integral code system for containment analysis (INCA) which includes in addition GASFLOW for distribution calculations, V3D for slow combustion and DET3D for detonation analysis. COM3D uses a TVD-solver and optional models for turbulence, chemistry and thermodynamics. The hydrodynamic model considers mass, momentum and energy conservation. Advanced procedures were provided to facilitate grid-development for complex 3-d structures. COM3D was validated on experiments performed on different scales with generally good agreement for important physical quantities. The code was applied to combustion analysis of a large PWR. The initial conditions were obtained from a GASFLOW distribution analysis for a LOOP scenario. Results are presented concerning flame propagation and pressure evolution in the containment which clearly demonstrate the effects of internal structures, their influence on turbulence formation and consequences for local loads. (author)

3D-Printed Bioactive Ca3SiO5 Bone Cement Scaffolds with Nano Surface Structure for Bone Regeneration.

Science.gov (United States)

Yang, Chen; Wang, Xiaoya; Ma, Bing; Zhu, Haibo; Huan, Zhiguang; Ma, Nan; Wu, Chengtie; Chang, Jiang

2017-02-22

Silicate bioactive materials have been widely studied for bone regeneration because of their eminent physicochemical properties and outstanding osteogenic bioactivity, and different methods have been developed to prepare porous silicate bioactive ceramics scaffolds for bone-tissue engineering applications. Among all of these methods, the 3D-printing technique is obviously the most efficient way to control the porous structure. However, 3D-printed bioceramic porous scaffolds need high-temperature sintering, which will cause volume shrinkage and reduce the controllability of the pore structure accuracy. Unlike silicate bioceramic, bioactive silicate cements such as tricalcium silicate (Ca 3 SiO 5 and C 3 S) can be self-set in water to obtain high mechanical strength under mild conditions. Another advantage of using C 3 S to prepare 3D scaffolds is the possibility of simultaneous drug loading. Herein, we, for the first time, demonstrated successful preparation of uniform 3D-printed C 3 S bone cement scaffolds with controllable 3D structure at room temperature. The scaffolds were loaded with two model drugs and showed a loading location controllable drug-release profile. In addition, we developed a surface modification process to create controllable nanotopography on the surface of pore wall of the scaffolds, which showed activity to enhance rat bone-marrow stem cells (rBMSCs) attachment, spreading, and ALP activities. The in vivo experiments revealed that the 3D-printed C 3 S bone cement scaffolds with nanoneedle-structured surfaces significantly improved bone regeneration, as compared to pure C 3 S bone cement scaffolds, suggesting that 3D-printed C 3 S bone cement scaffolds with controllable nanotopography surface are bioactive implantable biomaterials for bone repair.

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

DEFF Research Database (Denmark)

Nielsen, Morten; Lundegaard, Claus; Lund, Ole

2010-01-01

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

3D Face modeling using the multi-deformable method.

Science.gov (United States)

Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

2012-09-25

In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper.

3D structure of individual nanocrystals in solution by electron microscopy

Science.gov (United States)

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.

Image fusion in craniofacial virtual reality modeling based on CT and 3dMD photogrammetry.

Science.gov (United States)

Xin, Pengfei; Yu, Hongbo; Cheng, Huanchong; Shen, Shunyao; Shen, Steve G F

2013-09-01

The aim of this study was to demonstrate the feasibility of building a craniofacial virtual reality model by image fusion of 3-dimensional (3D) CT models and 3 dMD stereophotogrammetric facial surface. A CT scan and stereophotography were performed. The 3D CT models were reconstructed by Materialise Mimics software, and the stereophotogrammetric facial surface was reconstructed by 3 dMD patient software. All 3D CT models were exported as Stereo Lithography file format, and the 3 dMD model was exported as Virtual Reality Modeling Language file format. Image registration and fusion were performed in Mimics software. Genetic algorithm was used for precise image fusion alignment with minimum error. The 3D CT models and the 3 dMD stereophotogrammetric facial surface were finally merged into a single file and displayed using Deep Exploration software. Errors between the CT soft tissue model and 3 dMD facial surface were also analyzed. Virtual model based on CT-3 dMD image fusion clearly showed the photorealistic face and bone structures. Image registration errors in virtual face are mainly located in bilateral cheeks and eyeballs, and the errors are more than 1.5 mm. However, the image fusion of whole point cloud sets of CT and 3 dMD is acceptable with a minimum error that is less than 1 mm. The ease of use and high reliability of CT-3 dMD image fusion allows the 3D virtual head to be an accurate, realistic, and widespread tool, and has a great benefit to virtual face model.

Automatic balancing of 3D models

DEFF Research Database (Denmark)

Christiansen, Asger Nyman; Schmidt, Ryan; Bærentzen, Jakob Andreas

2014-01-01

3D printing technologies allow for more diverse shapes than are possible with molds and the cost of making just one single object is negligible compared to traditional production methods. However, not all shapes are suitable for 3D print. One of the remaining costs is therefore human time spent......, in these cases, we will apply a rotation of the object which only deforms the shape a little near the base. No user input is required but it is possible to specify manufacturing constraints related to specific 3D print technologies. Several models have successfully been balanced and printed using both polyjet...... is solved by creating cavities of air and distributing dense materials inside the model. Consequently, the surface is not deformed. However, printing materials with significantly different densities is often not possible and adding cavities of air is often not enough to make the model balance. Consequently...

A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

Science.gov (United States)

Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl

2016-08-01

The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci. Copyright © 2016 Elsevier B.V. All rights reserved.

e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design.

Science.gov (United States)

Pihan, Emilie; Colliandre, Lionel; Guichou, Jean-François; Douguet, Dominique

2012-06-01

In the drug discovery field, new uses for old drugs, selective optimization of side activities and fragment-based drug design (FBDD) have proved to be successful alternatives to high-throughput screening. e-Drug3D is a database of 3D chemical structures of drugs that provides several collections of ready-to-screen SD files of drugs and commercial drug fragments. They are natural inputs in studies dedicated to drug repurposing and FBDD. e-Drug3D collections are freely available at http://chemoinfo.ipmc.cnrs.fr/e-drug3d.html either for download or for direct in silico web-based screenings.

The Value of 3D Printing Models of Left Atrial Appendage Using Real-Time 3D Transesophageal Echocardiographic Data in Left Atrial Appendage Occlusion: Applications toward an Era of Truly Personalized Medicine.

Science.gov (United States)

Liu, Peng; Liu, Rijing; Zhang, Yan; Liu, Yingfeng; Tang, Xiaoming; Cheng, Yanzhen

The objective of this study was to assess the clinical feasibility of generating 3D printing models of left atrial appendage (LAA) using real-time 3D transesophageal echocardiogram (TEE) data for preoperative reference of LAA occlusion. Percutaneous LAA occlusion can effectively prevent patients with atrial fibrillation from stroke. However, the anatomical structure of LAA is so complicated that adequate information of its structure is essential for successful LAA occlusion. Emerging 3D printing technology has the demonstrated potential to structure more accurately than conventional imaging modalities by creating tangible patient-specific models. Typically, 3D printing data sets are acquired from CT and MRI, which may involve intravenous contrast, sedation, and ionizing radiation. It has been reported that 3D models of LAA were successfully created by the data acquired from CT. However, 3D printing of the LAA using real-time 3D TEE data has not yet been explored. Acquisition of 3D transesophageal echocardiographic data from 8 patients with atrial fibrillation was performed using the Philips EPIQ7 ultrasound system. Raw echocardiographic image data were opened in Philips QLAB and converted to 'Cartesian DICOM' format and imported into Mimics® software to create 3D models of LAA, which were printed using a rubber-like material. The printed 3D models were then used for preoperative reference and procedural simulation in LAA occlusion. We successfully printed LAAs of 8 patients. Each LAA costs approximately CNY 800-1,000 and the total process takes 16-17 h. Seven of the 8 Watchman devices predicted by preprocedural 2D TEE images were of the same sizes as those placed in the real operation. Interestingly, 3D printing models were highly reflective of the shape and size of LAAs, and all device sizes predicted by the 3D printing model were fully consistent with those placed in the real operation. Also, the 3D printed model could predict operating difficulty and the