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Sample records for model 3-d structure

  1. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

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

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-01

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

  5. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  6. 3D Modeling of Branching Structures for Anatomical Instruction

    PubMed Central

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

    2015-01-01

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

  7. Ground and Structure Deformation 3d Modelling with a Tin Based Property Model

    NASA Astrophysics Data System (ADS)

    TIAN, T.; Zhang, J.; Jiang, W.

    2013-12-01

    With the development of 3D( three-dimensional) modeling and visualization, more and more 3D tectonics are used to assist the daily work in Engineering Survey, in which the prediction of deformation field in strata and structure induced by underground construction is an essential part. In this research we developed a TIN (Triangulated Irregular Network) based property model for the 3D (three dimensional) visualization of ground deformation filed. By record deformation vector for each nodes, the new model can express the deformation with geometric-deformation-style by drawing each node in its new position and deformation-attribute-distribution-style by drawing each node in the color correspond with its deformation attribute at the same time. Comparing with the volume model based property model, this new property model can provide a more precise geometrical shape for structure objects. Furthermore, by recording only the deformation data of the user-interested 3d surface- such as the ground surface or the underground digging surface, the new property model can save a lot of space, which makes it possible to build the deformation filed model of a much more large scale. To construct the models of deformation filed based on TIN model, the refinement of the network is needed to increase the nodes number, which is necessary to express the deformation filed with a certain resolution. The TIN model refinement is a process of sampling the 3D deformation field values on points on the TIN surface, for which we developed a self-adapting TIN refinement method. By set the parameter of the attribute resolution, this self-adapting method refines the input geometric-expressing TIN model by adding more vertexes and triangles where the 3D deformation filed changing faster. Comparing with the even refinement method, the self-adapting method can generate a refined TIN model with nodes counted less by two thirds. Efficiency Comparison between Self-adapting Refinement Method and Even

  8. 3D Fluid-Structure Modeling of a Monofin

    NASA Astrophysics Data System (ADS)

    Monier, L.; Razafimahery, F.; Rakotomanana, L.

    2010-10-01

    The purpose of this paper is to develop a numerical modelisation for the behaviour of a monofin. We have developped a fluid struture model simulating the movement of a fin in a swimming pool. We first present the geometry and the equations and then proceed to different numerical experiments in order to validate the model.

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

    PubMed

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. Mathematical structure of the three-dimensional (3D) Ising model

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

    An overview of the mathematical structure of the three-dimensional (3D) Ising model is given from the points of view of topology, algebra, and geometry. By analyzing the relationships among transfer matrices of the 3D Ising model, Reidemeister moves in the knot theory, Yang-Baxter and tetrahedron equations, the following facts are illustrated for the 3D Ising model. 1) The complex quaternion basis constructed for the 3D Ising model naturally represents the rotation in a (3+1)-dimensional space-time as a relativistic quantum statistical mechanics model, which is consistent with the 4-fold integrand of the partition function obtained by taking the time average. 2) A unitary transformation with a matrix that is a spin representation in 2n·l·o-space corresponds to a rotation in 2n·l·o-space, which serves to smooth all the crossings in the transfer matrices and contributes the non-trivial topological part of the partition function of the 3D Ising model. 3) A tetrahedron relationship would ensure the commutativity of the transfer matrices and the integrability of the 3D Ising model, and its existence is guaranteed by the Jordan algebra and the Jordan-von Neumann-Wigner procedures. 4) The unitary transformation for smoothing the crossings in the transfer matrices changes the wave functions by complex phases varphix, varphiy, and varphiz. The relationship with quantum field and gauge theories and the physical significance of the weight factors are discussed in detail. The conjectured exact solution is compared with numerical results, and the singularities at/near infinite temperature are inspected. The analyticity in β = 1/(kBT) of both the hard-core and the Ising models has been proved only for β > 0, not for β = 0. Thus the high-temperature series cannot serve as a standard for judging a putative exact solution of the 3D Ising model.

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

    PubMed

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

    2016-07-01

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb. PMID:27095203

  15. Modelling and analysing 3D buildings with a primal/dual data structure

    NASA Astrophysics Data System (ADS)

    Boguslawski, Pawel; Gold, Christopher M.; Ledoux, Hugo

    While CityGML permits us to represent 3D city models, its use for applications where spatial analysis and/or real-time modifications are required is limited since at this moment the possibility to store topological relationships between the elements is rather limited and often not exploited. We present in this paper a new topological data structure, the dual half-edge (DHE), which permits us to represent the topology of 3D buildings (including their interiors) and of the surrounding terrain. It is based on the idea of simultaneously storing a graph in 3D space and its dual graph, and to link the two. We propose Euler-type operators for incrementally constructing 3D models (for adding individual edges, faces and volumes to the model while updating the dual structure simultaneously), and we also propose navigation operators to move from a given point to all the connected planes or polyhedra for example. The DHE also permits us to store attributes to any element. We have implemented the DHE and have tested it with different CityGML models. Our technique allows us to handle important query types, for example finding the nearest exterior exit to a given room, as in disaster management planning. As the structure is locally modifiable the model may be adapted whenever a particular pathway is no longer available. The proposed DHE structure adds significant analytic value to the increasingly popular CityGML model.

  16. Seismic source inversion using Green's reciprocity and a 3-D structural model for the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Simutė, S.; Fichtner, A.

    2015-12-01

    We present a feasibility study for seismic source inversions using a 3-D velocity model for the Japanese Islands. The approach involves numerically calculating 3-D Green's tensors, which is made efficient by exploiting Green's reciprocity. The rationale for 3-D seismic source inversion has several aspects. For structurally complex regions, such as the Japan area, it is necessary to account for 3-D Earth heterogeneities to prevent unknown structure polluting source solutions. In addition, earthquake source characterisation can serve as a means to delineate existing faults. Source parameters obtained for more realistic Earth models can then facilitate improvements in seismic tomography and early warning systems, which are particularly important for seismically active areas, such as Japan. We have created a database of numerically computed 3-D Green's reciprocals for a 40°× 40°× 600 km size area around the Japanese Archipelago for >150 broadband stations. For this we used a regional 3-D velocity model, recently obtained from full waveform inversion. The model includes attenuation and radial anisotropy and explains seismic waveform data for periods between 10 - 80 s generally well. The aim is to perform source inversions using the database of 3-D Green's tensors. As preliminary steps, we present initial concepts to address issues that are at the basis of our approach. We first investigate to which extent Green's reciprocity works in a discrete domain. Considering substantial amounts of computed Green's tensors we address storage requirements and file formatting. We discuss the importance of the initial source model, as an intelligent choice can substantially reduce the search volume. Possibilities to perform a Bayesian inversion and ways to move to finite source inversion are also explored.

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

    PubMed Central

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site. PMID:26257525

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

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

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

  19. A reduced-coordinate approach to modeling RNA 3-D structures

    SciTech Connect

    Tung, Chang-Shung

    1997-09-01

    With the realization of RNA molecules capable of performing very specific functions (e.g., catalytic RNAs and RNAs that bind ligand with affinity and specificity of an anti-body) and contrary to the traditional view that structure of RNA molecules being functionally passive, it has become clear that studying the 3-dimensional (3-D) folding of RNA molecules is a very important task. In the absence of sufficient number of experimentally determined RNA structures available up-to-date, folding of RNA structures computationally provides an alternative approach in studying the 3-D structure of RNA molecules. We have developed a computational approach for folding RNA 3-D structures. The method is conceptually simple and general. It consists of two major components. The first being the arrangement of all helices in space. Once the helices are positioned and oriented in space, structures of the connecting loops are modeled and inserted between the helices. Any number of structural constraints derived either experimentally or theoretically can be used to guide the folding processes. A conformational sampling approach is developed with structural equilibration using the Metropolis Monte Carlo simulation. The lengths of various loop sizes (ranging from 1 base to 7 bases) are calculated based on a set of RNA structures deposited in PDB as well as a set of loop structures constructed using our method. The validity of using the averaged loop lengths of the connecting loops as distance constraints for arranging the helices in space is studied.

  20. Computer modeling of 3D structures of cytochrome P450s.

    PubMed

    Chang, Y T; Stiffelman, O B; Loew, G H

    1996-01-01

    The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified. PMID:9010606

  1. Modeling tumor/polyp/lesion structure in 3D for computer-aided diagnosis in colonoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Chao-I.; Sargent, Dusty; Wang, Yuan-Fang

    2010-02-01

    We describe a software system for building three-dimensional (3D) models from colonoscopic videos. The system is end-to-end in the sense that it takes as input raw image frames-shot during a colon exam-and produces the 3D structure of objects of interest (OOI), such as tumors, polyps, and lesions. We use the structure-from-motion (SfM) approach in computer vision which analyzes an image sequence in which camera's position and aim vary relative to the OOI. The varying pose of the camera relative to the OOI induces the motion-parallax effect which allows 3D depth of the OOI to be inferred. Unlike the traditional SfM system pipeline, our software system contains many check-and-balance mechanisms to ensure robustness, and the analysis from earlier stages of the pipeline is used to guide the later processing stages to better handle challenging medical data. The constructed 3D models allow the pathology (growth and change in both structure and appearance) to be monitored over time.

  2. 3D interactive model of lumbar spinal structures of anesthetic interest.

    PubMed

    Prats-Galino, Alberto; Reina, Miguel A; Mavar Haramija, Marija; Puigdellivol-Sánchez, Anna; Juanes Méndez, Juan A; De Andrés, José A

    2015-03-01

    A 3D model of lumbar structures of anesthetic interest was reconstructed from human magnetic resonance (MR) images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The MR images were analyzed using a specific 3D software platform for biomedical data. Models generated from manually delimited volumes of interest and selected MR images were exported to Virtual Reality Modeling Language format and were presented in a PDF document containing JavaScript-based functions. The 3D file and the corresponding instructions and license files can be downloaded freely at http://diposit.ub.edu/dspace/handle/2445/44844?locale=en. The 3D PDF interactive file includes reconstructions of the L3-L5 vertebrae, intervertebral disks, ligaments, epidural and foraminal fat, dural sac and nerve root cuffs, sensory and motor nerve roots of the cauda equina, and anesthetic approaches (epidural medial, spinal paramedial, and selective nerve root paths); it also includes a predefined sequential educational presentation. Zoom, 360° rotation, selective visualization, and transparency graduation of each structure and clipping functions are available. Familiarization requires no specialized informatics knowledge. The ease with which the document can be used could make it valuable for anatomical and anesthetic teaching and demonstration of patient information. PMID:25352014

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  4. Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

    NASA Astrophysics Data System (ADS)

    Qin, W.; Yang, L.

    2004-05-01

    Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

  5. Enhanced hybrid search algorithm for protein structure prediction using the 3D-HP lattice model.

    PubMed

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

    2013-09-01

    The problem of protein structure prediction in the hydrophobic-polar (HP) lattice model is the prediction of protein tertiary structure. This problem is usually referred to as the protein folding problem. This paper presents a method for the application of an enhanced hybrid search algorithm to the problem of protein folding prediction, using the three dimensional (3D) HP lattice model. The enhanced hybrid search algorithm is a combination of the particle swarm optimizer (PSO) and tabu search (TS) algorithms. Since the PSO algorithm entraps local minimum in later evolution extremely easily, we combined PSO with the TS algorithm, which has properties of global optimization. Since the technologies of crossover and mutation are applied many times to PSO and TS algorithms, so enhanced hybrid search algorithm is called the MCMPSO-TS (multiple crossover and mutation PSO-TS) algorithm. Experimental results show that the MCMPSO-TS algorithm can find the best solutions so far for the listed benchmarks, which will help comparison with any future paper approach. Moreover, real protein sequences and Fibonacci sequences are verified in the 3D HP lattice model for the first time. Compared with the previous evolutionary algorithms, the new hybrid search algorithm is novel, and can be used effectively to predict 3D protein folding structure. With continuous development and changes in amino acids sequences, the new algorithm will also make a contribution to the study of new protein sequences. PMID:23824509

  6. Dynamic Characteristics of a Model and Prototype for 3D-RC Structure

    NASA Astrophysics Data System (ADS)

    Moniuddin, Md. Khaja; Vasanthalakshmi, G.; Chethan, K.; Babu, R. Ramesh

    2016-06-01

    Infill walls provide durable and economical partitions that have relatively excellent thermal and sound insulation with high fire resistance. Monolithic infilled walls are provided within RC structures without being analyzed as a combination of concrete and brick elements, although in reality they act as a single unit during earthquakes. The performance of such structures during earthquakes has proved to be superior in comparison to bare frames in terms of stiffness, strength and energy dissipation. To know the dynamic characteristics of monolithic infill wall panels and masonry infill, modal, response spectrum and time history analyses have been carried out on a model and prototype of a 3D RC structure for a comparative study.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  9. Predicting RNA 3D structure using a coarse-grain helix-centered model

    PubMed Central

    Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2015-01-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

  10. 3D structural model of the North Alpine Foreland Basin, Bavarian Part

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2013-04-01

    The continental collision of Europe and Africa leads to the rise of the European Alps, which gave way to the formation of the North Alpine Foreland Basin, also referred to as the Molasse Basin, since the Tertiary. This typically wedge formed "foredeep" basin is filled with predominantly clastic sediments originating from erosional processes of the Alps which overly a southward dipping Mesozoic and Paleozoic succession. With our project we want to contribute to the understanding of the structure and subsequently of the thermal configuration of the Molasse Basin and its underlying deposits on a basin wide scale. We constructed a 3D structural model of the basin down to the crust-mantle-boundary, beginning with the Bavarian part. Therefore we used an approach of already existing local to midscale 2D and 3D structural models (e.g. Lüschen et al. 2006) as well as surface maps, seismic, well and gravity data. This 3D structural model resolves 5 sedimentary layers of the Mesozoic, including the geothermally utilized carbonate Malm aquifer (e.g. Birner et al. 2011), as well as the combined Paleozoic basement. Assuming isostatic equilibrium of the system a lithosphere-asthenosphere-boundary (LAB) has been calculated and compared to other published LABs of the region. Subsequently the model has been further constrained by 3D gravity modeling. The outcomes show that Cretaceous sediments are restricted to a small region in the central to eastern model area and are mostly overlain by the Tertiary Molasse sediments. The Triassic sediments occur in the northern and western part of the model area and do not continue far under the Molasse basin proper, while the Jurassic can be tracked as far south as beneath the Alps. The evaluation of the gravity indicates that the crystalline crust consists of a lighter upper crust and a denser lower crust. Our final LAB is shallowest under the Triassic subbasin, descending below the Bohemian Massif and the Molasse Basin proper and rising again

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Dolžan, Erazem; Vrabec, Marko

    2015-04-01

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

  13. Cross modality registration of video and magnetic tracker data for 3D appearance and structure modeling

    NASA Astrophysics Data System (ADS)

    Sargent, Dusty; Chen, Chao-I.; Wang, Yuan-Fang

    2010-02-01

    The paper reports a fully-automated, cross-modality sensor data registration scheme between video and magnetic tracker data. This registration scheme is intended for use in computerized imaging systems to model the appearance, structure, and dimension of human anatomy in three dimensions (3D) from endoscopic videos, particularly colonoscopic videos, for cancer research and clinical practices. The proposed cross-modality calibration procedure operates this way: Before a colonoscopic procedure, the surgeon inserts a magnetic tracker into the working channel of the endoscope or otherwise fixes the tracker's position on the scope. The surgeon then maneuvers the scope-tracker assembly to view a checkerboard calibration pattern from a few different viewpoints for a few seconds. The calibration procedure is then completed, and the relative pose (translation and rotation) between the reference frames of the magnetic tracker and the scope is determined. During the colonoscopic procedure, the readings from the magnetic tracker are used to automatically deduce the pose (both position and orientation) of the scope's reference frame over time, without complicated image analysis. Knowing the scope movement over time then allows us to infer the 3D appearance and structure of the organs and tissues in the scene. While there are other well-established mechanisms for inferring the movement of the camera (scope) from images, they are often sensitive to mistakes in image analysis, error accumulation, and structure deformation. The proposed method using a magnetic tracker to establish the camera motion parameters thus provides a robust and efficient alternative for 3D model construction. Furthermore, the calibration procedure does not require special training nor use expensive calibration equipment (except for a camera calibration pattern-a checkerboard pattern-that can be printed on any laser or inkjet printer).

  14. Pore - to - Core Modeling of Soil Organic Matter Decomposition in 3D Soil Structures

    NASA Astrophysics Data System (ADS)

    Falconer, R. E.; Battaia, G.; Baveye, P.; Otten, W.

    2013-12-01

    There is a growing body of literature supporting the need for microbial contributions to be considered explicitly in carbon-climate models. There is also overwhelming evidence that physical protection within aggregates can play a significant role in organic matter dynamics. Yet current models of soil organic matter dynamics divide soil organic matter into conceptual pools with distinct turnover times, assuming that a combination of biochemical and physical properties control decay without explicit description. Albeit robust in their application, such models are not capable to account for changes in soil structure or microbial populations, or accurately predict the effect of wetness or priming. A spatially explicit model is presented that accounts for microbial dynamics and physical processes, permitting consideration of the heterogeneity of the physical and chemical microenvironments at scales relevant for microbes. Exemplified for fungi, we investigate how micro-scale processes manifest at the core scale with particular emphasis on evolution of CO2 and biomass distribution. The microbial model is based upon previous (Falconer et al, 2012) and includes the following processes: uptake, translocation, recycling, enzyme production, growth, spread and respiration. The model is parameterised through a combination of literature data and parameter estimation (Cazelles et al., 2012).The Carbon model comprises two pools, particulate organic matter which through enzymatic activity is converted into dissolved organic matter. The microbial and carbon dynamics occur within a 3D soil structure obtained by X-ray CT. We show that CO2 is affected not only by the amount of Carbon in the soil but also by microbial dynamics, soil structure and the spatial distribution of OM. The same amount of OM can result in substantially different respiration rates, with surprisingly more CO2 with increased clustering of OM. We can explain this from the colony dynamics, production of enzymes and

  15. Assessment of the isostatic state and the load distribution of the European Molasse basin by means of lithospheric-scale 3D structural and 3D gravity modelling

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2015-07-01

    The European Molasse basin is a foreland basin situated at the northern front of the European Alps and has formed as a consequence of the Euro-Adriatic continental collision since the Tertiary. Today, it is underlain by Mesozoic sedimentary successions on top of a Paleozoic crust. To investigate the deep structure, the isostatic state, as well as the load distribution in the basin and the adjacent Alpine area, we constructed a lithospheric-scale 3D structural model by implementing available surface, well and seismic data. Subsequently, the structure of the model was constrained by means of 3D gravity modelling. Complementary, the isostatic state has been assessed based on the calculation of the 3D load distribution. Our results show that the Molasse basin is not in isostatic equilibrium and that the gravity field of the area is strongly controlled by the configuration of the crystalline crust. Furthermore, we show that the area is influenced by significant lateral load variations down to a depth of -150 km, which are considerably larger than commonly assumed for this level. Furthermore, our results allow a first-order assessment of the minimum compensating horizontal stress required to prevent gravitational collapse.

  16. 3D modeling method for computer animate based on modified weak structured light method

    NASA Astrophysics Data System (ADS)

    Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

    2010-11-01

    A simple and affordable 3D scanner is designed in this paper. Three-dimensional digital models are playing an increasingly important role in many fields, such as computer animate, industrial design, artistic design and heritage conservation. For many complex shapes, optical measurement systems are indispensable to acquiring the 3D information. In the field of computer animate, such an optical measurement device is too expensive to be widely adopted, and on the other hand, the precision is not as critical a factor in that situation. In this paper, a new cheap 3D measurement system is implemented based on modified weak structured light, using only a video camera, a light source and a straight stick rotating on a fixed axis. For an ordinary weak structured light configuration, one or two reference planes are required, and the shadows on these planes must be tracked in the scanning process, which destroy the convenience of this method. In the modified system, reference planes are unnecessary, and size range of the scanned objects is expanded widely. A new calibration procedure is also realized for the proposed method, and points cloud is obtained by analyzing the shadow strips on the object. A two-stage ICP algorithm is used to merge the points cloud from different viewpoints to get a full description of the object, and after a series of operations, a NURBS surface model is generated in the end. A complex toy bear is used to verify the efficiency of the method, and errors range from 0.7783mm to 1.4326mm comparing with the ground truth measurement.

  17. The 3D structure of QCD and the roots of the Standard Model

    NASA Astrophysics Data System (ADS)

    Mulders, P. J.

    2016-03-01

    For many phenomenological applications involving hadrons in high energy processes the hadronic structure can be taken care of by parton distribution functions (PDFs), in which only the collinear momenta of quarks and gluons are important. In principle the transverse structure, however, provides interesting new phenomenology. Taking into account transverse momenta of partons one works with transverse momentum dependent PDFs (TMDs), These allow all spin-spin correlations and also spin-orbit correlations that have a time reversal odd character and lead to new observables. In many theoretical developments the link to the collinear treatment is used. In this talk I will speculate on a novel view of the 3-dimensional (3D) structure of QCD, which fits in a broader study looking at the roots of the Standard Model of particle physics.

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

    NASA Astrophysics Data System (ADS)

    Giacomini, B. B.

    2014-12-01

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

  19. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

    PubMed

    Meier, Armin; Söding, Johannes

    2015-10-01

    Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite. PMID:26496371

  20. Representing geometric structures in 3D tomography soil images: Application to pore-space modeling

    NASA Astrophysics Data System (ADS)

    Monga, Olivier; Ndeye Ngom, Fatou; François Delerue, Jean

    2007-09-01

    Only in the last decade have geoscientists started to use 3D computed tomography (CT) images of soil for better understanding and modeling of soil properties. In this paper, we propose one of the first approaches to allow the definition and computation of stable (intrinsic) geometric representations of structures in 3D CT soil images. This addresses the open problem set by the description of volume shapes from discrete traces without any a priori information. The basic concept involves representing the volume shape by a piecewise approximation using simple volume primitives (bowls, cylinders, cones, etc.). This typical representation is assumed to optimize a criterion ensuring its stability. This criterion includes the representation scale, which characterizes the trade-off between the fitting error and the number of patches. We also take into account the preservation of topological properties of the initial shape: the number of connected components, adjacency relationships, etc. We propose an efficient computation method for this piecewise approximation using cylinders or bowls. For cylinders, we use optimal region growing in a valuated adjacency graph that represents the primitives and their adjacency relationships. For bowls, we compute a minimal set of Delaunay spheres recovering the skeleton. Our method is applied to modeling of a coarse pore space extracted from 3D CT soil images. The piecewise bowls approximation gives a geometric formalism corresponding to the intuitive notion of pores and also an efficient way to compute it. This geometric and topological representation of coarse pore space can be used, for instance, to simulate biological activity in soil.

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

    NASA Astrophysics Data System (ADS)

    Przybycin, Anna M.; Scheck-Wenderoth, Magdalena; Schneider, Michael

    2014-05-01

    The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International

  2. Tactical 3D model generation using structure-from-motion on video from unmanned systems

    NASA Astrophysics Data System (ADS)

    Harguess, Josh; Bilinski, Mark; Nguyen, Kim B.; Powell, Darren

    2015-05-01

    Unmanned systems have been cited as one of the future enablers of all the services to assist the warfighter in dominating the battlespace. The potential benefits of unmanned systems are being closely investigated -- from providing increased and potentially stealthy surveillance, removing the warfighter from harms way, to reducing the manpower required to complete a specific job. In many instances, data obtained from an unmanned system is used sparingly, being applied only to the mission at hand. Other potential benefits to be gained from the data are overlooked and, after completion of the mission, the data is often discarded or lost. However, this data can be further exploited to offer tremendous tactical, operational, and strategic value. To show the potential value of this otherwise lost data, we designed a system that persistently stores the data in its original format from the unmanned vehicle and then generates a new, innovative data medium for further analysis. The system streams imagery and video from an unmanned system (original data format) and then constructs a 3D model (new data medium) using structure-from-motion. The 3D generated model provides warfighters additional situational awareness, tactical and strategic advantages that the original video stream lacks. We present our results using simulated unmanned vehicle data with Google Earth™providing the imagery as well as real-world data, including data captured from an unmanned aerial vehicle flight.

  3. High-resolution 3D seismic model of the crustal and uppermost mantle structure in Poland

    NASA Astrophysics Data System (ADS)

    Grad, Marek; Polkowski, Marcin; Ostaficzuk, Stanisław R.

    2016-01-01

    In the area of Poland a contact between the Precambrian and Phanerozoic Europe and the Carpathians has a complicated structure and a complex P-wave velocity of the sedimentary cover, crystalline crust, Moho depth and the uppermost mantle. The geometry of the uppermost several kilometers of sediments is relatively well recognized from over 100,000 boreholes. The vertical seismic profiling (VSP) from 1188 boreholes provided detailed velocity data for regional tectonic units and for stratigraphic successions from Permian to the Tertiary and Quaternary deposits. These data, however, do not provide information about the velocity and basement depth in the central part of the Trans-European suture zone (TESZ) and in the Carpathians. So, the data set is supplemented by 2D velocity models from 32 deep seismic sounding refraction profiles which also provide information about the crust and uppermost mantle. Together with the results of other methods: vertical seismic profiling, magnetotelluric, allow for the creation of a detailed, high-resolution 3D model for the entire Earth's crust and the uppermost mantle down to a depth of 60 km. The thinnest sedimentary cover in the Mazury-Belarus anteclise is only 0.3 to 1 km thick, which increases to 7 to 8 km along the East European Craton (EEC) margin, and 9 to 12 km in the TESZ. The Variscan domain is characterized by a 1-4 km thick sedimentary cover, while the Carpathians are characterized by very thick sedimentary layers, up to about 20 km. The crystalline crust is differentiated and has a layered structure. The crust beneath the West European Platform (WEP; Variscan domain) is characterized by P-wave velocities of 5.8-6.6 km/s. The upper and middle crusts beneath the EEC are characterized by velocities of 6.1-6.6 km/s, and are underlain by a high velocity lower crust with a velocity of about 7 km/s. A general decrease in velocity is observed from the older to the younger tectonic domains. The TESZ is associated with a steep dip

  4. 3D Whole-prominence Fine Structure Modeling. II. Prominence Evolution

    NASA Astrophysics Data System (ADS)

    Gunár, Stanislav; Mackay, Duncan H.

    2015-10-01

    We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing position of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.

  5. Modeling the effects of 3-D slab geometry and oblique subduction on subduction zone thermal structure

    NASA Astrophysics Data System (ADS)

    Wada, I.; Wang, K.; He, J.

    2013-12-01

    In this study, we revisit the effects of along-strike variation in slab geometry and oblique subduction on subduction zone thermal structures. Along-strike variations in slab dip cause changes in the descending rate of the slab and generate trench-parallel pressure gradients that drive trench-parallel mantle flow (e.g., Kneller and van Keken, 2007). Oblique subduction also drives trench-parallel mantle flow. In this study, we use a finite element code PGCtherm3D and examine a range of generic subduction geometries and parameters to investigate the effects of the above two factors. This exercise is part of foundational work towards developing detailed 3-D thermal models for NE Japan, Nankai, and Cascadia to better constrain their 3-D thermal structures and to understand the role of temperature in controlling metamorphic, seismogenic, and volcanic processes. The 3-D geometry of the subducting slabs in the forearc and arc regions are well delineated at these three subduction zones. Further, relatively large compilations of surface heat flow data at these subduction zones make them excellent candidates for this study. At NE Japan, a megathrust earthquake occurred on March 11, 2011; at Nankai and Cascadia, there has been a great effort to constrain the scale of the next subduction thrust earthquake for the purpose of disaster prevention. Temperature influences the slip behavior of subduction faults by (1) affecting the rheology of the interface material and (2) controlling dehydration reactions, which can lead to elevated pore fluid pressure. Beyond the depths of subduction thrust earthquakes, the thermal structure is affected strongly by the pattern of mantle wedge flow. This flow is driven by viscous coupling between the subducting slab and the overriding mantle, and it brings in hot flowing mantle into the wedge. The trench-ward (up-dip) extent of the slab-mantle coupling is thus a key factor that controls the thermal structure. Slab-mantle decoupling at shallow

  6. Transition zone structure beneath NE China from 3D waveform modelling: Subduction related plumes

    NASA Astrophysics Data System (ADS)

    Tang, Y.; Grand, S. P.; Niu, F.

    2013-12-01

    Seismic tomography is currently used to image deep structure on global and local scales. However, tomography inversions usually underestimate amplitudes and likely cannot resolve narrow slow anomalies in the deep mantle. Careful modelling of waveform distortions has the potential to provide better constraints on small scale anomalies in the mantle. We observed strong waveform distortions from several earthquakes that propagated through a low velocity anomaly in the mantle transition zone beneath the Changbaishan volcanic center, Northeast China. The slow anomaly was recently found by tomography results using the NECESSArray. For each earthquake, there exists a cluster of stations whose S-wave amplitude is substantially higher than the other stations. Also, at the stations near the edges of the cluster, the recorded S waves become more complex, usually featuring two pulses with smaller amplitude. We used the spectral-element method (SPECFEM3D) to construct 3D waveforms using the tomographic model as a starting input model. Synthetic modeling indicated that the observed large amplitude and double arrivals for each cluster can be explained by a strong low velocity anomaly with a diameter of ~200 km surrounded by high velocities in the transition zone. The velocity contrast between the slow anomaly and the surrounding medium is at least 8%, which is double that found in the original tomographic model. The large velocity contrast (8%) cannot be the velocity contrast between the slab and normal transition zone mantle because if this were the case a travel time misfit with observed data to the west would result in. We speculate that the slow anomaly is a manifestation of a return flow upwelling through a slab gap in the mantle transition zone that feeds Changbaishan volcanism. The upwelling mantle is likely hot, and the heat source may come from warm, buoyant sub-lithospheric mantle entrained with the sinking lithosphere that requires an opening to rise.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. 3D Modelling of Inaccessible Areas using UAV-based Aerial Photography and Structure from Motion

    NASA Astrophysics Data System (ADS)

    Obanawa, Hiroyuki; Hayakawa, Yuichi; Gomez, Christopher

    2014-05-01

    In hardly accessible areas, the collection of 3D point-clouds using TLS (Terrestrial Laser Scanner) can be very challenging, while airborne equivalent would not give a correct account of subvertical features and concave geometries like caves. To solve such problem, the authors have experimented an aerial photography based SfM (Structure from Motion) technique on a 'peninsular-rock' surrounded on three sides by the sea at a Pacific coast in eastern Japan. The research was carried out using UAS (Unmanned Aerial System) combined with a commercial small UAV (Unmanned Aerial Vehicle) carrying a compact camera. The UAV is a DJI PHANTOM: the UAV has four rotors (quadcopter), it has a weight of 1000 g, a payload of 400 g and a maximum flight time of 15 minutes. The camera is a GoPro 'HERO3 Black Edition': resolution 12 million pixels; weight 74 g; and 0.5 sec. interval-shot. The 3D model has been constructed by digital photogrammetry using a commercial SfM software, Agisoft PhotoScan Professional®, which can generate sparse and dense point-clouds, from which polygonal models and orthophotographs can be calculated. Using the 'flight-log' and/or GCPs (Ground Control Points), the software can generate digital surface model. As a result, high-resolution aerial orthophotographs and a 3D model were obtained. The results have shown that it was possible to survey the sea cliff and the wave cut-bench, which are unobservable from land side. In details, we could observe the complexity of the sea cliff that is nearly vertical as a whole while slightly overhanging over the thinner base. The wave cut bench is nearly flat and develops extensively at the base of the cliff. Although there are some evidences of small rockfalls at the upper part of the cliff, there is no evidence of very recent activity, because no fallen rock exists on the wave cut bench. This system has several merits: firstly lower cost than the existing measuring methods such as manned-flight survey and aerial laser

  9. Learning structured models for segmentation of 2-D and 3-D imagery.

    PubMed

    Lucchi, Aurelien; Marquez-Neila, Pablo; Becker, Carlos; Li, Yunpeng; Smith, Kevin; Knott, Graham; Fua, Pascal

    2015-05-01

    Efficient and accurate segmentation of cellular structures in microscopic data is an essential task in medical imaging. Many state-of-the-art approaches to image segmentation use structured models whose parameters must be carefully chosen for optimal performance. A popular choice is to learn them using a large-margin framework and more specifically structured support vector machines (SSVM). Although SSVMs are appealing, they suffer from certain limitations. First, they are restricted in practice to linear kernels because the more powerful nonlinear kernels cause the learning to become prohibitively expensive. Second, they require iteratively finding the most violated constraints, which is often intractable for the loopy graphical models used in image segmentation. This requires approximation that can lead to reduced quality of learning. In this paper, we propose three novel techniques to overcome these limitations. We first introduce a method to "kernelize" the features so that a linear SSVM framework can leverage the power of nonlinear kernels without incurring much additional computational cost. Moreover, we employ a working set of constraints to increase the reliability of approximate subgradient methods and introduce a new way to select a suitable step size at each iteration. We demonstrate the strength of our approach on both 2-D and 3-D electron microscopic (EM) image data and show consistent performance improvement over state-of-the-art approaches. PMID:25438309

  10. Modelling of 3D Attenuation Structure in the Mantle Using a Waveform Approach: Successes and Challenges

    NASA Astrophysics Data System (ADS)

    Romanowicz, B. A.; Gung, Y.

    2003-12-01

    The study of lateral variations in Q in the upper mantle at the global scale is generally addressed using isolated phases in the seismogram (for example fundamental mode surface wave spectra), which limits the sampling and therefore the resolution of Q structure that can be achieved. The use of isolated phases has the advantage of working directly with amplitudes, thus making it easier to detect contamination of the anelastic attenuation signal by elastic focusing and scattering, a key problem in attenuation tomography. We here discuss recent progress on a waveform modeling approach, which allows us to work with entire seismograms and exploit the information contained both in fundamental mode surface waves, overtones and body waves. The method is based on a normal mode approach and proceeds iteratively. In the first step, we invert for 3D elastic structure using the NACT approach (Non-linear Asymptotic Coupling Theory; Li and Romanowicz, 1995), which aligns the phase part of the observed and synthetic seismograms. In the second step, we invert for Q. The crucial issue is how to account for elastic effects in the amplitudes (focusing)- we discuss asymptotic versus more exact methods to address this problem and illustrate the effects on the resulting models. We discuss prominent features in the lateral variations in Q in the upper mantle, their evolution with depth, and their relation with elastic structure, in particular from the point of view of resolving upwellings and the large scale signature of plumes.

  11. 3D modeling of soil structure in urban groundwater areas: case studies in Kolpene, Rovaniemi, Finland

    NASA Astrophysics Data System (ADS)

    Kupila, Juho

    2015-04-01

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

  12. 3D-graphite structure

    SciTech Connect

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

    2011-01-15

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

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

    PubMed Central

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    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-(phenylthio)thymine 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. PMID:27399692

  14. Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.

    PubMed

    Putz, Mihai V; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    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-(phenylthio)thymine 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. PMID:27399692

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  16. 2D and 3D multipactor modeling in dielectric-loaded accelerator structures

    NASA Astrophysics Data System (ADS)

    Sinitsyn, Oleksandr; Nusinovich, Gregory; Antonsen, Thomas

    2010-11-01

    Multipactor (MP) is known as the avalanche growth of the number of secondary electrons emitted from a solid surface exposed to an RF electric field under vacuum conditions. MP is a severe problem in modern rf systems and, therefore, theoretical and experimental studies of MP are of great interest to the researchers working in various areas of physics and engineering. In this work we present results of MP studies in dielectric-loaded accelerator (DLA) structures. First, we show simulation results obtained with the use of the 2D self-consistent MP model (O. V. Sinitsyn, et. al., Phys. Plasmas, vol. 16, 073102 (2009)) and compare those to experimental ones obtained during recent extensive studies of DLA structures performed by Argonne National Laboratory, Naval Research Laboratory, SLAC National Accelerator Laboratory and Euclid TechLabs (C. Jing, et al., IEEE Trans. Plasma Sci., vol. 38, pp. 1354-1360 (2010)). Then we present some new results of 3D analysis of MP which include studies of particle trajectories and studies of MP development at the early stage.

  17. A Generalized Functional Model Based Method for Vibration-Based Damage Precise Localization in 3D Structures

    NASA Astrophysics Data System (ADS)

    Sakaris, Christos S.; Sakellariou, John S.; Fassois, Spilios D.

    2015-07-01

    A Generalized Functional Model Based Method for vibration-based damage precise localization on structures consisting of 1D, 2D, or 3D elements is introduced. The method generalizes previous versions applicable to structures consisting of 1D elements, thus allowing for 2D and 3D elements as well. It is based on scalar (single sensor) or vector (multiple sensor) Functional Models which - in the inspection phase - incorporate the mathematical form of the specific structural topology. Precise localization is then based on coordinate estimation within this model structure, and confidence bounds are also obtained. The effectiveness of the method is demonstrated through experiments on a 3D truss structure where damage corresponds to single bolt loosening. Both the scalar and vector versions of the method are shown to be effective even within a very limited, low frequency, bandwidth of 3-59 Hz. The improvement achieved through the use of multiple sensors is also demonstrated.

  18. Designing stream restoration structures using 3D hydro-morphodynamic numerical modeling

    NASA Astrophysics Data System (ADS)

    Khosronejad, A.; Kozarek, J. L.; Hill, C.; Kang, S.; Plott, R.; Diplas, P.; Sotiropoulos, F.

    2012-12-01

    Efforts to stabilize and restore streams and rivers across the nation have grown dramatically in the last fifteen years, with over $1 billion spent every year since 1990. The development of effective and long-lasting strategies, however, is far from trivial and despite large investments it is estimated that at least 50% of stream restoration projects fail. This is because stream restoration is today more of an art than a science. The lack of physics-based engineering standards for stream restoration techniques is best underscored in the design and installation of shallow, in-stream, low-flow structures, which direct flow away from the banks, protect stream banks from erosion and scour, and increase habitat diversity. Present-day design guidelines for such in-stream structures are typically vague and rely heavily on empirical knowledge and intuition rather than physical understanding of the interactions of the structures the flow and sediment transport processes in the waterway. We have developed a novel computer-simulation based paradigm for designing in stream structures that is based on state-of-the-art 3D hydro-morphodynamic modeling validated with laboratory and field-scale experiments. The numerical model is based on the Curvilinear Immersed Boundary (CURVIB) approach of Kang et al. and Khosronejad et al. (Adv. in Water Res. 2010, 2011), which can simulate flow and sediment transport processes in arbitrarily complex waterways with embedded rock structures. URANS or large-eddy simulation (LES) models are used to simulate turbulence. Transport of bed materials is simulated using the non-equilibrium Exner equation for the bed surface elevation coupled with a transport equation for suspended load. Extensive laboratory and field-scale experiments have been carried out and employed to validate extensively the computational model. The numerical model is used to develop a virtual testing environment within which one or multiple in-stream structures can be embedded in

  19. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect

    SciTech Connect

    Shi, Ya-Zhou; Wang, Feng-Hua; Wu, Yuan-Yan; Tan, Zhi-Jie

    2014-09-14

    To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the room/body temperature and high salt (1M NaCl), and thus generally hardly predict the thermodynamics and salt effect. In this study, we propose a coarse-grained model with implicit salt for RNAs to predict 3D structures, stability, and salt effect. Combined with Monte Carlo simulated annealing algorithm and a coarse-grained force field, the model folds 46 tested RNAs (≤45 nt) including pseudoknots into their native-like structures from their sequences, with an overall mean RMSD of 3.5 Å and an overall minimum RMSD of 1.9 Å from the experimental structures. For 30 RNA hairpins, the present model also gives the reliable predictions for the stability and salt effect with the mean deviation ∼ 1.0 °C of melting temperatures, as compared with the extensive experimental data. In addition, the model could provide the ensemble of possible 3D structures for a short RNA at a given temperature/salt condition.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  1. Modeling the Impact of Drizzle and 3D Cloud Structure on Remote Sensing of Effective Radius

    NASA Technical Reports Server (NTRS)

    Platnick, Steven; Zinner, Tobias; Ackerman, S.

    2008-01-01

    Remote sensing of cloud particle size with passive sensors like MODIS is an important tool for cloud microphysical studies. As a measure of the radiatively relevant droplet size, effective radius can be retrieved with different combinations of visible through shortwave infrared channels. MODIS observations sometimes show significantly larger effective radii in marine boundary layer cloud fields derived from the 1.6 and 2.1 pm channel observations than for 3.7 pm retrievals. Possible explanations range from 3D radiative transport effects and sub-pixel cloud inhomogeneity to the impact of drizzle formation on the droplet distribution. To investigate the potential influence of these factors, we use LES boundary layer cloud simulations in combination with 3D Monte Carlo simulations of MODIS observations. LES simulations of warm cloud spectral microphysics for cases of marine stratus and broken stratocumulus, each for two different values of cloud condensation nuclei density, produce cloud structures comprising droplet size distributions with and without drizzle size drops. In this study, synthetic MODIS observations generated from 3D radiative transport simulations that consider the full droplet size distribution will be generated for each scene. The operational MODIS effective radius retrievals will then be applied to the simulated reflectances and the results compared with the LES microphysics.

  2. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  4. Properties of the prominence magnetic field and plasma distributions as obtained from 3D whole-prominence fine structure modeling

    NASA Astrophysics Data System (ADS)

    Gunár, S.; Mackay, D. H.

    2016-07-01

    Aims: We analyze distributions of the magnetic field strength and prominence plasma (temperature, pressure, plasma β, and mass) using the 3D whole-prominence fine structure model. Methods: The model combines a 3D magnetic field configuration of an entire prominence, obtained from non-linear force-free field simulations, with a detailed semi-empirically derived description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Results: We show that in the modeled prominence, the variations of the magnetic field strength and its orientation are insignificant on scales comparable to the smallest dimensions of the observed prominence fine structures. We also show the ability of the 3D whole-prominence fine structure model to reveal the distribution of the prominence plasma with respect to its temperature within the prominence volume. This provides new insights into the composition of the prominence-corona transition region. We further demonstrate that the values of the plasma β are small throughout the majority of the modeled prominences when realistic photospheric magnetic flux distributions and prominence plasma parameters are assumed. While this is generally true, we also find that in the region with the deepest magnetic dips, the plasma β may increase towards unity. Finally, we show that the mass of the modeled prominence plasma is in good agreement with the mass of observed non-eruptive prominences.

  5. 3D Modeling of Lacus Mortis Pit Crater with Presumed Interior Tube Structure

    NASA Astrophysics Data System (ADS)

    Hong, Ik-Seon; Yi, Yu; Yu, Jaehyung; Haruyama, Junichi

    2015-06-01

    When humans explore the Moon, lunar caves will be an ideal base to provide a shelter from the hazards of radiation, meteorite impact, and extreme diurnal temperature differences. In order to ascertain the existence of caves on the Moon, it is best to visit the Moon in person. The Google Lunar X Prize(GLXP) competition started recently to attempt lunar exploration missions. Ones of those groups competing, plan to land on a pit of Lacus Mortis and determine the existence of a cave inside this pit. In this pit, there is a ramp from the entrance down to the inside of the pit, which enables a rover to approach the inner region of the pit. In this study, under the assumption of the existence of a cave in this pit, a 3D model was developed based on the optical image data. Since this model simulates the actual terrain, the rendering of the model agrees well with the image data. Furthermore, the 3D printing of this model will enable more rigorous investigations and also could be used to publicize lunar exploration missions with ease.

  6. Reinterpretation of nappe structures in the Central Alps Evidence from 3D foliation field modelling

    NASA Astrophysics Data System (ADS)

    Maxelon, M.; Mancktelow, N. S.

    2003-04-01

    The Lepontine Alps represent the classic region for both, fold nappe development at mid-crustal levels and fold interference patterns from outcrop to regional scale. They have also been proposed as models for rapid burial and exhumation. However, before such models can be applied or critically assessed, the geometry of the units involved must be accurately known in three dimensions and this is a challenging task in this complex region. The three-dimensional geometry of the Lepontine nappes is not established unequivocally, as the integration and visualisation of structural data reflecting at least five different deformation phases has not yet been achieved satisfactorily. The present study focusses on a combination of new structural mapping in critical and/or contradictory areas, existing observations and their geostatistical assessment with modern computer-based tools (Editeur Géologique, Gocad) in order to develop a testable three-dimensional model of the geometry of the Lepontine Nappes in the Central Alps. Here we present a regional-scale three dimensional model of the southern central part of the Lepontine Region, bordered by the Swiss-Italian frontier in the east and Valle Leventina to the west and by Biasca and Locarno to the north and south. The model visualises a geostatistical calculation of the dominant foliation field in three dimensions, based on field measurements. The present day tectonostratigraphy and nappe geometry are mainly influenced by the three earliest recognisable Alpine deformation phases D_1 to D_3. D_1 structures are associated with first-time crustal nappe emplacement. Lithologies that are interpreted as nappe separators - mainly Mesozoic sediments such as "Bündnerschiefer" - have mostly been interleaved between the nappes during D_1, which entails strong isoclinal folding and pronounced boudinage of the infolded lithologies, with the development of a penetrative foliation S_1. S_1 and the infolded Mesozoic have been intensely

  7. In vitro model of the epidermis: Connecting protein function to 3D structure

    PubMed Central

    Arnette, Christopher; Koetsier, Jennifer L.; Hoover, Paul; Getsios, Spiro; Green, Kathleen J.

    2016-01-01

    Overview Much of our understanding of the biological processes that underlie cellular functions in humans, such as cell-cell communication, intracellular signaling, and transcriptional and post-transcriptional control of gene expression, has been acquired from studying cells in a two-dimensional (2D) tissue culture environment. However, it has become increasingly evident that the 2D environment does not support certain cell functions. The need for more physiologically relevant models prompted the development of three-dimensional (3D) cultures of epithelial, endothelial and neuronal tissues (Shamir and Ewald 2014). These models afford investigators with powerful tools to study the contribution of spatial organization, often in the context of relevant extracellular matrix and stromal components, to cellular and tissue homeostasis in normal and disease states. PMID:26778564

  8. Influence of Young's moduli in 3D fluid-structure coupled models of the human cochlea

    NASA Astrophysics Data System (ADS)

    Böhnke, Frank; Semmelbauer, Sebastian; Marquardt, Torsten

    2015-12-01

    The acoustic wave propagation in the human cochlea was studied using a tapered box-model with linear assumptions respective to all mechanical parameters. The discretisation and evaluation is conducted by a commercial finite element package (ANSYS). The main difference to former models of the cochlea was the representation of the basilar membrane by a 3D elastic solid. The Young's moduli of this solid were modified to study their influence on the travelling wave. The lymph in the scala vestibuli and scala tympani was represented by a viscous and nearly incompressible fluid finite element approach. Our results show the maximum displacement for f = 2kHz at half of the length of the cochlea in accordance with former experiments. For low frequencies f <200 Hz nearly zero phase shifts were found, whereas for f =1 kHz it reaches values up to -12 cycles depending on the degree of orthotropy.

  9. A study of the effects of degraded imagery on tactical 3D model generation using structure-from-motion

    NASA Astrophysics Data System (ADS)

    Bolick, Leslie; Harguess, Josh

    2016-05-01

    An emerging technology in the realm of airborne intelligence, surveillance, and reconnaissance (ISR) systems is structure-from-motion (SfM), which enables the creation of three-dimensional (3D) point clouds and 3D models from two-dimensional (2D) imagery. There are several existing tools, such as VisualSFM and open source project OpenSfM, to assist in this process, however, it is well-known that pristine imagery is usually required to create meaningful 3D data from the imagery. In military applications, such as the use of unmanned aerial vehicles (UAV) for surveillance operations, imagery is rarely pristine. Therefore, we present an analysis of structure-from-motion packages on imagery that has been degraded in a controlled manner.

  10. 3-D Waveguide Effects of Topographical Structural Variation on Full Waveform Propagation: 3-D Finite Difference Modeling Comparisons with Field Data From Yuma Proving Ground, Arizona

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

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

  11. 3D printing of high-resolution PLA-based structures by hybrid electrohydrodynamic and fused deposition modeling techniques

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Seong, Baekhoon; Nguyen, VuDat; Byun, Doyoung

    2016-02-01

    Recently, the three-dimensional (3D) printing technique has received much attention for shape forming and manufacturing. The fused deposition modeling (FDM) printer is one of the various 3D printers available and has become widely used due to its simplicity, low-cost, and easy operation. However, the FDM technique has a limitation whereby its patterning resolution is too low at around 200 μm. In this paper, we first present a hybrid mechanism of electrohydrodynamic jet printing with the FDM technique, which we name E-FDM. We then develop a novel high-resolution 3D printer based on the E-FDM process. To determine the optimal condition for structuring, we also investigated the effect of several printing parameters, such as temperature, applied voltage, working height, printing speed, flow-rate, and acceleration on the patterning results. This method was capable of fabricating both high resolution 2D and 3D structures with the use of polylactic acid (PLA). PLA has been used to fabricate scaffold structures for tissue engineering, which has different hierarchical structure sizes. The fabrication speed was up to 40 mm/s and the pattern resolution could be improved to 10 μm.

  12. Making Inexpensive 3-D Models

    NASA Astrophysics Data System (ADS)

    Manos, Harry

    2016-03-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the TPT theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity well tailored to specific class lessons. Most of the supplies are readily available in the home or at school: rubbing alcohol, a rag, two colors of spray paint, art brushes, and masking tape. The cost of these supplies, if you don't have them, is less than 20.

  13. 3D model reconstruction of underground goaf

    NASA Astrophysics Data System (ADS)

    Fang, Yuanmin; Zuo, Xiaoqing; Jin, Baoxuan

    2005-10-01

    Constructing 3D model of underground goaf, we can control the process of mining better and arrange mining work reasonably. However, the shape of goaf and the laneway among goafs are very irregular, which produce great difficulties in data-acquiring and 3D model reconstruction. In this paper, we research on the method of data-acquiring and 3D model construction of underground goaf, building topological relation among goafs. The main contents are as follows: a) The paper proposed an efficient encoding rule employed to structure the field measurement data. b) A 3D model construction method of goaf is put forward, which by means of combining several TIN (triangulated irregular network) pieces, and an efficient automatic processing algorithm of boundary of TIN is proposed. c) Topological relation of goaf models is established. TIN object is the basic modeling element of goaf 3D model, and the topological relation among goaf is created and maintained by building the topological relation among TIN objects. Based on this, various 3D spatial analysis functions can be performed including transect and volume calculation of goaf. A prototype is developed, which can realized the model and algorithm proposed in this paper.

  14. Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture

    PubMed Central

    Quaini, A.; Canic, S.; Glowinski, R.; Igo, S.; Hartley, C.J.; Zoghbi, W.; Little, S.

    2011-01-01

    This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194

  15. Validation of a 3D computational fluid-structure interaction model simulating flow through an elastic aperture.

    PubMed

    Quaini, A; Canic, S; Glowinski, R; Igo, S; Hartley, C J; Zoghbi, W; Little, S

    2012-01-10

    This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. PMID:22138194

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

    PubMed Central

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

    2013-01-01

    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. PMID:23395283

  17. 3D Segmentation of Rodent Brain Structures Using Hierarchical Shape Priors and Deformable Models

    PubMed Central

    Zhang, Shaoting; Huang, Junzhou; Uzunbas, Mustafa; Shen, Tian; Delis, Foteini; Huang, Xiaolei; Volkow, Nora; Thanos, Panayotis; Metaxas, Dimitris N.

    2016-01-01

    In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance. PMID:22003750

  18. 3D segmentation of rodent brain structures using hierarchical shape priors and deformable models.

    PubMed

    Zhang, Shaoting; Huang, Junzhou; Uzunbas, Mustafa; Shen, Tian; Delis, Foteini; Huang, Xiaolei; Volkow, Nora; Thanos, Panayotis; Metaxas, Dimitris N

    2011-01-01

    In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance. PMID:22003750

  19. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    PubMed

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure. PMID:23943281

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

    NASA Astrophysics Data System (ADS)

    Vollgger, Stefan; Cruden, Alexander

    2015-04-01

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

  1. Calibration and 3D reconstruction of underwater objects with non-single-view projection model by structured light stereo imaging.

    PubMed

    Wang, Yexin; Negahdaripour, Shahriar; Aykin, Murat D

    2016-08-20

    Establishing the projection model of imaging systems is critical in 3D reconstruction of object shapes from multiple 2D views. When deployed underwater, these are enclosed in waterproof housings with transparent glass ports that generate nonlinear refractions of optical rays at interfaces, leading to invalidation of the commonly assumed single-viewpoint (SVP) model. In this paper, we propose a non-SVP ray tracing model for the calibration of a projector-camera system, employed for 3D reconstruction based on the structured light paradigm. The projector utilizes dot patterns, having established that the contrast loss is less severe than for traditional stripe patterns in highly turbid waters. Experimental results are presented to assess the achieved calibrating accuracy. PMID:27556973

  2. Non-linear dynamic analysis of ancient masonry structures by 3D rigid block models

    NASA Astrophysics Data System (ADS)

    Orduña, Agustin; Ayala, A. Gustavo

    2015-12-01

    This work presents a formulation for non-linear dynamic analysis of unreinforced masonry structures using rigid block models. This procedure is akin to the distinct element family of methods, nevertheless, we assume that small displacements occur and, therefore, the formulation does not involve the search for new contacts between blocks. This proposal is also related to the rigid element method, although, in this case we use full three-dimensional models and a more robust interface formulation.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  4. 3D Modeling Engine Representation Summary Report

    SciTech Connect

    Steven Prescott; Ramprasad Sampath; Curtis Smith; Timothy Yang

    2014-09-01

    Computers have been used for 3D modeling and simulation, but only recently have computational resources been able to give realistic results in a reasonable time frame for large complex models. This summary report addressed the methods, techniques, and resources used to develop a 3D modeling engine to represent risk analysis simulation for advanced small modular reactor structures and components. The simulations done for this evaluation were focused on external events, specifically tsunami floods, for a hypothetical nuclear power facility on a coastline.

  5. A full 3D plane-wave-expansion model for 1-3 piezoelectric composite structures.

    PubMed

    Wilm, Mikaël; Ballandras, Sylvain; Laude, Vincent; Pastureaud, Thomas

    2002-09-01

    The plane-wave-expansion (PWE) approach dedicated to the simulation of periodic devices has been extended to 1-3 connectivity piezoelectric composite structures. The case of simple but actual piezoelectric composite structures is addressed, taking piezoelectricity, acoustic losses, and electrical excitation conditions rigorously into account. The material distribution is represented by using a bidimensional Fourier series and the electromechanical response is simulated using a Bloch-Floquet expansion together with the Fahmy-Adler formulation of the Christoffel problem. Application of the model to 1-3 connectivity piezoelectric composites is reported and compared to previously published analyses of this problem. PMID:12243182

  6. 3D active shape models of human brain structures: application to patient-specific mesh generation

    NASA Astrophysics Data System (ADS)

    Ravikumar, Nishant; Castro-Mateos, Isaac; Pozo, Jose M.; Frangi, Alejandro F.; Taylor, Zeike A.

    2015-03-01

    The use of biomechanics-based numerical simulations has attracted growing interest in recent years for computer-aided diagnosis and treatment planning. With this in mind, a method for automatic mesh generation of brain structures of interest, using statistical models of shape (SSM) and appearance (SAM), for personalised computational modelling is presented. SSMs are constructed as point distribution models (PDMs) while SAMs are trained using intensity profiles sampled from a training set of T1-weighted magnetic resonance images. The brain structures of interest are, the cortical surface (cerebrum, cerebellum & brainstem), lateral ventricles and falx-cerebri membrane. Two methods for establishing correspondences across the training set of shapes are investigated and compared (based on SSM quality): the Coherent Point Drift (CPD) point-set registration method and B-spline mesh-to-mesh registration method. The MNI-305 (Montreal Neurological Institute) average brain atlas is used to generate the template mesh, which is deformed and registered to each training case, to establish correspondence over the training set of shapes. 18 healthy patients' T1-weightedMRimages form the training set used to generate the SSM and SAM. Both model-training and model-fitting are performed over multiple brain structures simultaneously. Compactness and generalisation errors of the BSpline-SSM and CPD-SSM are evaluated and used to quantitatively compare the SSMs. Leave-one-out cross validation is used to evaluate SSM quality in terms of these measures. The mesh-based SSM is found to generalise better and is more compact, relative to the CPD-based SSM. Quality of the best-fit model instance from the trained SSMs, to test cases are evaluated using the Hausdorff distance (HD) and mean absolute surface distance (MASD) metrics.

  7. Study of materials and machines for 3D printed large-scale, flexible electronic structures using fused deposition modeling

    NASA Astrophysics Data System (ADS)

    Hwang, Seyeon

    The 3 dimensional printing (3DP), called to additive manufacturing (AM) or rapid prototyping (RP), is emerged to revolutionize manufacturing and completely transform how products are designed and fabricated. A great deal of research activities have been carried out to apply this new technology to a variety of fields. In spite of many endeavors, much more research is still required to perfect the processes of the 3D printing techniques especially in the area of the large-scale additive manufacturing and flexible printed electronics. The principles of various 3D printing processes are briefly outlined in the Introduction Section. New types of thermoplastic polymer composites aiming to specified functional applications are also introduced in this section. Chapter 2 shows studies about the metal/polymer composite filaments for fused deposition modeling (FDM) process. Various metal particles, copper and iron particles, are added into thermoplastics polymer matrices as the reinforcement filler. The thermo-mechanical properties, such as thermal conductivity, hardness, tensile strength, and fracture mechanism, of composites are tested to figure out the effects of metal fillers on 3D printed composite structures for the large-scale printing process. In Chapter 3, carbon/polymer composite filaments are developed by a simple mechanical blending process with an aim of fabricating the flexible 3D printed electronics as a single structure. Various types of carbon particles consisting of multi-wall carbon nanotube (MWCNT), conductive carbon black (CCB), and graphite are used as the conductive fillers to provide the thermoplastic polyurethane (TPU) with improved electrical conductivity. The mechanical behavior and conduction mechanisms of the developed composite materials are observed in terms of the loading amount of carbon fillers in this section. Finally, the prototype flexible electronics are modeled and manufactured by the FDM process using Carbon/TPU composite filaments and

  8. Rapid Centroid Moment Tensor (CMT) Inversion in 3D Earth Structure Model for Earthquakes in Southern California

    NASA Astrophysics Data System (ADS)

    Mu, D.; Lee, E.; Chen, P.; Jordan, T. H.; Maechling, P. J.

    2010-12-01

    Accurate and rapid CMT inversion is important for seismic hazard analysis. We have developed an algorithm for very rapid CMT inversions in a 3D Earth structure model and applied it on small to medium-sized earthquakes recorded by the Southern California Seismic Network (SCSN). Our CMT inversion algorithm is an integral component of the scattering-integral (SI) method for full-3D waveform tomography (F3DT). In the SI method for F3DT, the sensitivity (Fréchet) kernels are constructed through the temporal convolution between the earthquake wavefield (EWF) from the source and the receiver Green tensor (RGT) from the receiver. In this study, our RGTs were computed in a 3D seismic structure model for Southern California (CVM4SI1) using the finite-difference method, which allows us to account for 3D path effects in our source inversion. By storing the RGTs, synthetic seismograms for any source in our modeling volume could be generated rapidly by applying the reciprocity principle. An automated waveform-picking algorithm based on continuous wavelet transform is applied on observed waveforms to pick P, S and surface waves. A grid-searching algorithm is then applied on the picked waveforms to find an optimal focal mechanism that minimizes the amplitude misfit and maximize the weighted correlation coefficient. The grid-search result is then used as the initial solution in a gradient-based optimization algorithm that minimizes the L2 norm of the generalized seismological data functionals (GSDF), which quantifies waveform differences between observed and synthetic seismograms using frequencies-dependent phase-delay and amplitude anomalies. In general, our CMT solutions agree with solutions inverted using other methods and provide better fit to the observed waveforms.

  9. Modular 3-D Transport model

    EPA Science Inventory

    MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...

  10. Solar abundances and 3D model atmospheres

    NASA Astrophysics Data System (ADS)

    Ludwig, Hans-Günter; Caffau, Elisabetta; Steffen, Matthias; Bonifacio, Piercarlo; Freytag, Bernd; Cayrel, Roger

    2010-03-01

    We present solar photospheric abundances for 12 elements from optical and near-infrared spectroscopy. The abundance analysis was conducted employing 3D hydrodynamical (CO5BOLD) as well as standard 1D hydrostatic model atmospheres. We compare our results to others with emphasis on discrepancies and still lingering problems, in particular exemplified by the pivotal abundance of oxygen. We argue that the thermal structure of the lower solar photosphere is very well represented by our 3D model. We obtain an excellent match of the observed center-to-limb variation of the line-blanketed continuum intensity, also at wavelengths shortward of the Balmer jump.

  11. Crowdsourcing Based 3d Modeling

    NASA Astrophysics Data System (ADS)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

  12. Rapid Centroid Moment Tensor (CMT) Inversion in 3D Earth Structure Model for Earthquakes in Southern California

    NASA Astrophysics Data System (ADS)

    Chen, P.; Lee, E.; Jordan, T. H.; Maechling, P. J.

    2009-12-01

    Accurate and rapid CMT inversion is important for seismic hazard analysis. We have developed an algorithm for very rapid CMT inversions in a 3D Earth structure model and applied it on small to medium-sized earthquakes recorded by the Southern California Seismic Network (SCSN). Our CMT inversion algorithm is an integral component of the scattering-integral (SI) method for full-3D waveform tomography (F3DT). In the SI method for F3DT, the sensitivity (Fréchet) kernels are constructed through the temporal convolution between the earthquake wavefield (EWF) and the receiver Green tensor (RGT), which is the wavefield generated by 3 orthogonal unit impulsive body forces acting at the receiver location. The RGTs are also the partial derivatives of the waveform with respect to the moment tensors. In this study, our RGTs are computed in a 3D seismic structure model for Southern California (CVM4SI1) using the finite-difference method, which allows us to account for 3D path effects in our source inversion. We used three component broadband waveforms below 0.2 Hz. An automated waveform-picking algorithm based on continuous wavelet transform is applied on observed waveforms to pick P, S and surface waves. A multi-scale grid-searching algorithm is then applied on the picked waveforms to find the optimal strike, dip and rake values that minimize the amplitude misfit and maximize the correlation coefficient. In general, our CMT solutions agree with solutions inverted using other methods and provide better fit to the observed waveforms.

  13. Reverse modeling of 2D and 3D diapiric salt structures

    NASA Astrophysics Data System (ADS)

    Fernandez, N.; Kaus, B.

    2013-12-01

    Mechanical forward modeling of salt diapirs formed by two different processes (differential loading and buoyancy driven) has been widely performed with numerical codes in many studies, whereas works focusing on the dynamic retro-deformation of such structures remain scarce. Buoyancy driven diapirs, in which the density difference between salt and overburden induces upward motion of salt, have been successfully retro-deformed in two and three dimensions using simple rheologies for the salt and overburden (e.g., Kaus & Podladchikov 2001). However, retro-deformation of down-building diapirs (syndepositional process in which salt structures grow while sediments are being deposited) using mechanical codes has only been done in two dimensions (e.g., Ismael-Zadeh et al. 2001), even though the importance of three-dimensionality in salt diapirism is accepted. We have used the two-dimensional visco-elasto-plastic finite element code MILAMIN_VEP to perform both forward and backward simulations and to check the validity of a reversed time step method (Kaus & Podladchikov 2001 and Ismael-Zadeh et al. 2001) for a wide range of parameters, variable sedimentation rates, and for non-linear rheologies. Forward simulations are run until the salt layer is exhausted and then a reverse time step is applied in order to retro-deform the model. Down-building process was mimicked using a fast-erosion condition at the surface, which keeps it flat and redistributes material at every time step. Initially, we have tested our method by retro-deforming salt structures that develop from an interface that is sinusoidally perturbed. More realistic simulations were performed by starting with randomly perturbed salt interface and using different rheological parameters for the salt and the overburden as well as variable sedimentation rates. Once the method has been proved successful for different parameters in two dimensions, the finite differences parallel code LaMEM has also been used to dynamically

  14. Advanced 3D electromagnetic and particle-in-cell modeling on structured/unstructured hybrid grids

    SciTech Connect

    Seidel, D.B.; Pasik, M.F.; Kiefer, M.L.; Riley, D.J.; Turner, C.D.

    1998-01-01

    New techniques have been recently developed that allow unstructured, free meshes to be embedded into standard 3-dimensional, rectilinear, finite-difference time-domain grids. The resulting hybrid-grid modeling capability allows the higher resolution and fidelity of modeling afforded by free meshes to be combined with the simplicity and efficiency of rectilinear techniques. Integration of these new methods into the full-featured, general-purpose QUICKSILVER electromagnetic, Particle-In-Cell (PIC) code provides new modeling capability for a wide variety of electromagnetic and plasma physics problems. To completely exploit the integration of this technology into QUICKSILVER for applications requiring the self-consistent treatment of charged particles, this project has extended existing PIC methods for operation on these hybrid unstructured/rectilinear meshes. Several technical issues had to be addressed in order to accomplish this goal, including the location of particles on the unstructured mesh, adequate conservation of charge, and the proper handling of particles in the transition region between structured and unstructured portions of the hybrid grid.

  15. Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

    NASA Astrophysics Data System (ADS)

    Bulusu, Kartik V.; Plesniak, Michael W.

    2015-11-01

    In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

  16. Processes of Equatorial Thermal Structure: An Analysis of Galileo Temperature Profile with 3-D Model

    NASA Technical Reports Server (NTRS)

    Majeed, T.; Waite, J. H., Jr.; Bougher, S. W.; Gladstone, G. R.

    2005-01-01

    The Jupiter Thermosphere General Circulation Model (JTGCM) calculates the global dynamical structure of Jupiter's thermosphere self-consistently with its global thermal structure and composition. The main heat source that drives the thermospheric flow is high-latitude Joule heating. A secondary source of heating is the auroral process of particle precipitation. Global simulations of Jovian thermospheric dynamics indicate strong neutral outflows from the auroral ovals with velocities up to approximately 2 kilometers per second and subsequent convergence and downwelling at the Jovian equator. Such circulation is shown to be an important process for transporting significant amounts of auroral energy to equatorial latitudes and for regulating the global heat budget in a manner consistent with the high thermospheric temperatures observed by the Galileo probe. Adiabatic compression of the neutral atmosphere resulting from downward motion is an important source of equatorial heating (less than 0.06 microbar). The adiabatic heating continues to dominate between 0.06 and 0.2 microbar, but with an addition of comparable heating due to horizontal advection induced by the meridional flow. Thermal conduction plays an important role in transporting heat down to lower altitudes (greater than 0.2microbar) where it is balanced by the cooling associated with the wind transport processes. Interestingly, we find that radiative cooling caused by H3(+), CH4, and C2H2 emissions does not play a significant role in interpreting the Galileo temperature profile.

  17. 3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations 1. Chelsea soil humic acid.

    SciTech Connect

    Gassman, Paul; Hatcher, Patrick G.; Faulon, Jean-Loup Michel; Simpson, Andre; Goddard, William A., III; Diallo, Mamadou S.; Johnson, James H. Jr.

    2003-07-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D {sup 1}H and {sup 13}C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated {sup 13}C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  18. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  19. Influence of Chemical Piles on Convective Structure and the Geoid from 3D Spherical Mantle Convection Models

    NASA Astrophysics Data System (ADS)

    Liu, X.; Zhong, S.

    2013-12-01

    Classic mantle dynamic models for the Earth's geoid are mostly based on whole mantle convection and constrain that the upper mantle is significantly weaker than the lower mantle. Whole mantle convection models with such mantle viscosity structure have successfully explained the long-wavelength structure in the mantle. However, with increasing consensus on the existence of chemically distinct piles above the core mantle boundary (CMB) (also known as large low shear velocity provinces or LLSVPs), questions arise as to what extent the chemical piles influence the Earth's geoid and long-wavelength mantle convection. Some recent studies suggested that the chemical piles have a controlling effect on the Earth's degree two mantle structure, geoid, and true polar wander, although the chemical piles are estimated to be of small volume (~2% of the whole mantle) by seismic studies. We have formulated dynamically consistent 3D mantle convection models using CitcomS and studied how the chemical piles above CMB influence the long-wavelength convective structure and geoid. The models have free slip boundary conditions and temperature dependent viscosity. By comparing with purely thermal convection models, we found that the long wavelength convective structure is not sensitive to the presence of the chemical piles. By determining the geoid from the buoyance of a certain layer of the mantle, we found that for both purely thermal and thermochemical convection, the geoid is mostly contributed by the upper part of the mantle, with ~80% geoid explained by the buoyancy in the upper half of the mantle. In purely thermal convection, the contribution to the geoid from the bottom layer of the mantle always has the same sign with the total geoid (a bottom ~ 600 km thick layer gives ~3.5% of the total geoid). However, in the thermochemical convection, the bottom layer with overall negatively buoyant chemical piles gives rise to the geoid that has opposite sign with the total geoid and has a

  20. The Learner Characteristics, Features of Desktop 3D Virtual Reality Environments, and College Chemistry Instruction: A Structural Equation Modeling Analysis

    ERIC Educational Resources Information Center

    Merchant, Zahira; Goetz, Ernest T.; Keeney-Kennicutt, Wendy; Kwok, Oi-man; Cifuentes, Lauren; Davis, Trina J.

    2012-01-01

    We examined a model of the impact of a 3D desktop virtual reality environment on the learner characteristics (i.e. perceptual and psychological variables) that can enhance chemistry-related learning achievements in an introductory college chemistry class. The relationships between the 3D virtual reality features and the chemistry learning test as…

  1. Numerical Modeling of seismic wave propagation on Etna Volcano (Italy): Construction of 3D realistic velocity structures

    NASA Astrophysics Data System (ADS)

    Trovato, Claudio; Aochi, Hideo; De Martin, Florent

    2014-05-01

    Understanding the source mechanism of long-period (LP) seismic signals on volcanoes is an important key point in volcanology and for the hazard forecasting. In the last decades, moment tensor inversions have led to various descriptions of the kinematic source mechanism. These inversions suppose a relatively simple structure of the medium. However, the seismic wave propagation in a realistic 3-D volcano model should be taken into account for understanding the complicated physical processes of magma and gas behaviors at depth. We are studying Etna volcano, Italy, to understand the volcanic processes during different stages of activity. We adopt a spectral element method (SEM), a code EFISPEC3D (De Martin, BSSA, 2011), which shows a good accuracy and numerical stability in the simulations of seismic wave propagation. First we construct the geometrical model. We use a digital elevation model (DEM) to generate finite element meshes with a spacing of 50 m on the ground surface. We aim to calculate the ground motions until 3 Hz for the shallowest layer with Vs = ~500 m/s. The minimal size of the hexahedral elements is required to be around 100 m, with a total number of elements n = ~2 10 ^ 6 for the whole model. We compare different velocity structure configurations. We start with a homogeneous medium and add complexities taking in account the shallow low velocity structure. We also introduce a velocity gradient towards depth. Simulations performed in the homogeneous medium turn in approximately 20 hours for calculations parallelized on 16 CPUs. Complex velocity models should take approximately the same time of computation. We then try to simulate the ground motion from the LP sources (0.1-1.5 Hz) obtained by the inversion for the Etna volcano in 2008 (De Barros, GRL, 2009 and De Barros, JGR, 2011). Some vertical and horizontal structures can be added to reproduce injected dikes or sills respectively.

  2. 3D frequency modeling of elastic seismic wave propagation via a structured massively parallel direct Helmholtz solver

    NASA Astrophysics Data System (ADS)

    Wang, S.; De Hoop, M. V.; Xia, J.; Li, X.

    2011-12-01

    We consider the modeling of elastic seismic wave propagation on a rectangular domain via the discretization and solution of the inhomogeneous coupled Helmholtz equation in 3D, by exploiting a parallel multifrontal sparse direct solver equipped with Hierarchically Semi-Separable (HSS) structure to reduce the computational complexity and storage. In particular, we are concerned with solving this equation on a large domain, for a large number of different forcing terms in the context of seismic problems in general, and modeling in particular. We resort to a parsimonious mixed grid finite differences scheme for discretizing the Helmholtz operator and Perfect Matched Layer boundaries, resulting in a non-Hermitian matrix. We make use of a nested dissection based domain decomposition, and introduce an approximate direct solver by developing a parallel HSS matrix compression, factorization, and solution approach. We cast our massive parallelization in the framework of the multifrontal method. The assembly tree is partitioned into local trees and a global tree. The local trees are eliminated independently in each processor, while the global tree is eliminated through massive communication. The solver for the inhomogeneous equation is a parallel hybrid between multifrontal and HSS structure. The computational complexity associated with the factorization is almost linear with the size of the Helmholtz matrix. Our numerical approach can be compared with the spectral element method in 3D seismic applications.

  3. Internal structure and volcanic hazard potential of Mt Tongariro, New Zealand, from 3D gravity and magnetic models

    NASA Astrophysics Data System (ADS)

    Miller, Craig A.; Williams-Jones, Glyn

    2016-06-01

    A new 3D geophysical model of the Mt Tongariro Volcanic Massif (TgVM), New Zealand, provides a high resolution view of the volcano's internal structure and hydrothermal system, from which we derive implications for volcanic hazards. Geologically constrained 3D inversions of potential field data provides a greater level of insight into the volcanic structure than is possible from unconstrained models. A complex region of gravity highs and lows (± 6 mGal) is set within a broader, ~ 20 mGal gravity low. A magnetic high (1300 nT) is associated with Mt Ngauruhoe, while a substantial, thick, demagnetised area occurs to the north, coincident with a gravity low and interpreted as representing the hydrothermal system. The hydrothermal system is constrained to the west by major faults, interpreted as an impermeable barrier to fluid migration and extends to basement depth. These faults are considered low probability areas for future eruption sites, as there is little to indicate they have acted as magmatic pathways. Where the hydrothermal system coincides with steep topographic slopes, an increased likelihood of landslides is present and the newly delineated hydrothermal system maps the area most likely to have phreatic eruptions. Such eruptions, while small on a global scale, are important hazards at the TgVM as it is a popular hiking area with hundreds of visitors per day in close proximity to eruption sites. The model shows that the volume of volcanic material erupted over the lifespan of the TgVM is five to six times greater than previous estimates, suggesting a higher rate of magma supply, in line with global rates of andesite production. We suggest that our model of physical property distribution can be used to provide constraints for other models of dynamic geophysical processes occurring at the TgVM.

  4. The lithosphere-asthenosphere system beneath Ireland from integrated geophysical-petrological modeling II: 3D thermal and compositional structure

    NASA Astrophysics Data System (ADS)

    Fullea, J.; Muller, M. R.; Jones, A. G.; Afonso, J. C.

    2014-02-01

    The lithosphere-asthenosphere boundary (LAB) depth represents a fundamental parameter in any quantitative lithospheric model, controlling to a large extent the temperature distribution within the crust and the uppermost mantle. The tectonic history of Ireland includes early Paleozoic closure of the Iapetus Ocean across the Iapetus Suture Zone (ISZ), and in northeastern Ireland late Paleozoic to early Mesozoic crustal extension, during which thick Permo-Triassic sedimentary successions were deposited, followed by early Cenozoic extrusion of large scale flood basalts. Although the crustal structure in Ireland and neighboring offshore areas is fairly well constrained, with the notable exception of the crust beneath Northern Ireland, the Irish uppermost mantle remains to date relatively unknown. In particular, the nature and extent of a hypothetical interaction between a putative proto Icelandic mantle plume and the Irish and Scottish lithosphere during the Tertiary opening of the North Atlantic has long been discussed in the literature with diverging conclusions. In this work, the present-day thermal and compositional structure of the lithosphere in Ireland is modeled based on a geophysical-petrological approach (LitMod3D) that combines comprehensively a large variety of data (namely elevation, surface heat flow, potential fields, xenoliths and seismic tomography models), reducing the inherent uncertainties and trade-offs associated with classical modeling of those individual data sets. The preferred 3D lithospheric models show moderate lateral density variations in Ireland characterized by a slightly thickened lithosphere along the SW-NE trending ISZ, and a progressive lithospheric thinning from southern Ireland towards the north. The mantle composition in the southern half of Ireland (East Avalonia) is relatively and uniformly fertile (i.e., typical Phanerozoic mantle), whereas the lithospheric composition in the northern half of Ireland (Laurentia) seems to vary

  5. Pattern formation of down-built salt structures: insights from 3D numerical models

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris

    2015-04-01

    Many salt diapirs are thought to have formed as a result of down-building, which implies that the top of the diapir remained close to the surface during sediment deposition. This process is largely three-dimensional and in order to better understand what controls the patterns that form as a result of this down-building process, we here perform three-dimensional numerical models and compare the results with analytical models. In our models, we vary several parameters such as initial salt thickness, sedimentation rate, salt viscosity, salt-sediment viscosity contrast as well as the density of sediments. Down-building of three-dimensional diapirs only occurs for a certain range of parameters and is favored by lower sediment/salt viscosity contrasts and sedimentation rates in agreement with analytical predictions and findings from previous 2D models. However, the models show that the sedimentation rate has an additional effect on the formation and evolution of three-dimensional diapir patterns. At low sedimentation rates, salt ridges that form during early model stages remain preserved at later stages as well. For higher sedimentation rates, the initial salt ridges break up and form finger-like diapirs at the junction of salt ridges, which results in different salt exposure patterns at the surface. Once the initial pattern of diapirs is formed, higher sedimentation rate can also result in covered diapirs if the diapir extrusion velocity is insufficiently large. We quantify the effect of sedimentation rate on the number of diapirs exposed at the surface as well as on their spacing. In some cases, this final pattern is distinctly different from the initial polygonal pattern. We also study the extrusion of salt through time in the simulations, and show that it can be related to the geometries of the sedimentary layers surrounding the diapirs. Acknowledgements. Funding was provided by the European Research Council under the European Community's Seventh Framework Program

  6. Discovering Structural Regularity in 3D Geometry

    PubMed Central

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

    2010-01-01

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

  7. The Esri 3D city information model

    NASA Astrophysics Data System (ADS)

    Reitz, T.; Schubiger-Banz, S.

    2014-02-01

    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.

  8. Unit cell geometry of 3-D braided structures

    NASA Technical Reports Server (NTRS)

    Du, Guang-Wu; Ko, Frank K.

    1993-01-01

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

  9. 3D Models of Symbiotic Binaries

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Booth, R.; Podsiadlowski, Ph.; Ramstedt, S.; Vlemmings, W.; Maercker, M.

    2015-12-01

    Symbiotic binaries consist of a cool, mass-losing giant and an accreting, compact companion. We present 3D Smoothed Particle Hydrodynamics (SPH) models of two such interacting binaries, RS Oph and Mira AB. RS Oph is also a recurrent nova system, thus we model multiple quiescent mass transfer-nova outburst cycles. The resulting circumstellar structures of both systems are highly complex with the formation of spirals, arcs, shells, equatorial and bipolar outflows. We compare the models to recent observations and discuss the implications of our results for related systems, e.g., bipolar nebulae and jets, chemically peculiar stars, and the progenitors of Type Ia supernovae.

  10. Structured light field 3D imaging.

    PubMed

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

    2016-09-01

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

  11. Mapping tropical biodiversity using spectroscopic imagery : characterization of structural and chemical diversity with 3-D radiative transfer modeling

    NASA Astrophysics Data System (ADS)

    Feret, J. B.; Gastellu-Etchegorry, J. P.; Lefèvre-Fonollosa, M. J.; Proisy, C.; Asner, G. P.

    2014-12-01

    The accelerating loss of biodiversity is a major environmental trend. Tropical ecosystems are particularly threatened due to climate change, invasive species, farming and natural resources exploitation. Recent advances in remote sensing of biodiversity confirmed the potential of high spatial resolution spectroscopic imagery for species identification and biodiversity mapping. Such information bridges the scale-gap between small-scale, highly detailed field studies and large-scale, low-resolution satellite observations. In order to produce fine-scale resolution maps of canopy alpha-diversity and beta-diversity of the Peruvian Amazonian forest, we designed, applied and validated a method based on spectral variation hypothesis to CAO AToMS (Carnegie Airborne Observatory Airborne Taxonomic Mapping System) images, acquired from 2011 to 2013. There is a need to understand on a quantitative basis the physical processes leading to this spectral variability. This spectral variability mainly depends on canopy chemistry, structure, and sensor's characteristics. 3D radiative transfer modeling provides a powerful framework for the study of the relative influence of each of these factors in dense and complex canopies. We simulated series of spectroscopic images with the 3D radiative model DART, with variability gradients in terms of leaf chemistry, individual tree structure, spatial and spectral resolution, and applied methods for biodiversity mapping. This sensitivity study allowed us to determine the relative influence of these factors on the radiometric signal acquired by different types of sensors. Such study is particularly important to define the domain of validity of our approach, to refine requirements for the instrumental specifications, and to help preparing hyperspectral spatial missions to be launched at the horizon 2015-2025 (EnMAP, PRISMA, HISUI, SHALOM, HYSPIRI, HYPXIM). Simulations in preparation include topographic variations in order to estimate the robustness

  12. Integrated Biogeomorphological Modeling Using Delft3D

    NASA Astrophysics Data System (ADS)

    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.

  13. 3D Modeling of influence of oxygenated inflows on biogeochemical structure of redox-layer of enclosed seas

    NASA Astrophysics Data System (ADS)

    Podymov, O.

    2009-04-01

    In this study we used a coupled hydrophysical-biogeochemical model. Biogeochemical processes were described with O-N-S-P-Mn-Fe ROLM model (Yakushev et al, 2007), designed to study processes of organic matter (OM) formation and decay, reduction and oxidation of species of nitrogen, sulphur, manganese and iron, transformation of phosphorus species. Phytoplankton, zooplankton and bacteria were also parameterized and divided into four groups according to their relation to particular energy source and to OM transformation. Hydrophysical processes where described with 3D General Estuarine Transport Model (Burchard et al, 2004). We modeled the influence of oxygenated intrusions on the vertical biogeochemical structure of the central Gotland Sea. The model simulations demonstrate that a complete ventilation of the Gotland Deep bottom water caused by massive inflows of oxygenated North Sea water led to substantial changes of the vertical biogeochemical structure within this basin. During the inflow events large amounts of iron and manganese precipitate and discharge from the water column. In this phase redox reactions are accelerated and growth of bacteria leads to an increase of particulate matter content and consecutive particle sedimentation. An unbalanced structure of water column exists during the period of reestablishment of anoxic conditions. Its appearance is related to the absence of Mn species that play the dominant role in the oxidation-reduction reactions at the pelagic redox interfaces. This unbalanced structure can serve as a biotope for a development of untypical microbial redox-cline reactions (i.e. anammox). According to the model simulations the duration of the reestablishment period for a steady state of biogeochemistry after a complete flushing is about 1.5 years.

  14. 3D modelling of a dolomitized syn-sedimentary structure: an exhumed potential analogue of hydrocarbon reservoir.

    NASA Astrophysics Data System (ADS)

    Martinelli, Mattia; Franceschi, Marco; Massironi, Matteo; Bistacchi, Andrea; Di Cuia, Raffaele; Rizzi, Alessandro

    2016-04-01

    further increase the potential creation of potential hydrocarbon traps. These complex conditions are visible in a syn-sedimentary structure spectacularly exposed on the Monte Testo (Trentino, Italy). In this contribution, we present a 3D geo-model of this structure, obtained with SKUA-gOcad, based on 3D photogrammetric modelling, detailed geological mapping and structural analysis, porosity analysis carried out on representative sections, and geostatistical simulation of porosity on dolomitized bodies. Thanks to the 3D model we obtained: i) a thickness map of the Rotzo Formation that allow us to understand which faults were active during the deposition of the formation and which areas could have been more suitable for hydrocarbon accumulation; ii) a geometric and volumetric model of the structure that permitted us to study the porosity distribution and to define the potential volume of hydrocarbons that could be hosted by a similar structure. These results were eventually extrapolated to the entire platform, providing clues on the hydrocarbon potential of similar buried geologic bodies.

  15. 3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

    SciTech Connect

    Diallo, Mamadou S.; Simpson, Andre; Gassman, Paul L.; Faulon, Jean Loup; Johnson, Jr., James H.; Goddard, III, William A.; Hatcher, Patrick G.

    2003-05-01

    This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D | 1H and 13C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated 13C NMR spectrum of * Corresponding author phone: (626)395-2730; fax: (626)585-0918; e-mail: diallo@wag.caltech.edu and mdiallo@howard.edu. Present address: Materials and Process Simulation Center,BeckmanInstitute 139-74, California Institute of Technology, Pasadena, CA 91125. † California Institute of Technology. ‡ Howard University. § University of Toronto. Pacific Northwest National Laboratory. ^ Sandia National Laboratories. # The Ohio State University. ã xxxx American Chemical Society PAGE EST: 11 10.1021/es0259638 CCC: $25.00 Published on Web 00/00/0000 an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA.

  16. The geothermal field below the city of Berlin, Germany: Results from structurally and parametrically improved 3D Models

    NASA Astrophysics Data System (ADS)

    Frick, Maximilian; Sippel, Judith; Cacace, Mauro; Scheck-Wenderoth, Magdalena

    2016-04-01

    The goal of this study was to quantify the influence of the geological structure and geophysical parametrization of model units on the geothermal field as calculated by 3D numerical simulations of coupled fluid and heat transport for the subsurface of Berlin, Germany. The study area is located in the Northeast German Basin which is filled with several kilometers of sediments. This sedimentary infill includes the clastic sedimentary units Middle Buntsandstein and Sedimentary Rotliegend which are of particular interest for geothermal exploration. Previous studies conducted in the Northeast German Basin have already shown the geometries and properties of the geological units majorly control the distribution of subsurface temperatures. In this study we followed a two-step approach, where we first improved an existing structural model by integrating newly available 57 geological cross-sections, well data and deep seismics (down to ~4 km). Secondly, we performed a sensitivity analysis investigating the effects of varying physical fluid and rock properties on the subsurface temperature field. The results of this study show, that the structural configuration of model units exerts the highest influence on the geothermal field (up to ± 23 K at 1000 m below sea level). Here, the Rupelian clay aquitard, displaying a heterogeneous thickness distribution, locally characterized by hydrogeological windows (i.e. domains of no thickness) enabling intra-aquifer groundwater circulation has been identified as major controlling factor. The new structural configuration of this unit (more continuous, less numerous hydrogeological windows) also leads to a reduction of the influence of different boundary conditions and heat transport mechanisms considered. Additionally, the models results show that calculated temperatures highly depend on geophysical properties of model units whereas the hydraulic conductivity of the Cenozoic succession was identified as most dominant, leading to changes

  17. 3D modeling of optically challenging objects.

    PubMed

    Park, Johnny; Kak, Avinash

    2008-01-01

    We present a system for constructing 3D models of real-world objects with optically challenging surfaces. The system utilizes a new range imaging concept called multi-peak range imaging, which stores multiple candidates of range measurements for each point on the object surface. The multiple measurements include the erroneous range data caused by various surface properties that are not ideal for structured-light range sensing. False measurements generated by spurious reflections are eliminated by applying a series of constraint tests. The constraint tests based on local surface and local sensor visibility are applied first to individual range images. The constraint tests based on global consistency of coordinates and visibility are then applied to all range images acquired from different viewpoints. We show the effectiveness of our method by constructing 3D models of five different optically challenging objects. To evaluate the performance of the constraint tests and to examine the effects of the parameters used in the constraint tests, we acquired the ground truth data by painting those objects to suppress the surface-related properties that cause difficulties in range sensing. Experimental results indicate that our method significantly improves upon the traditional methods for constructing reliable 3D models of optically challenging objects. PMID:18192707

  18. Enhancing 3-D cell structures in confocal and STED microscopy: a joint model for interpolation, deblurring and anisotropic smoothing

    NASA Astrophysics Data System (ADS)

    Persch, Nico; Elhayek, Ahmed; Welk, Martin; Bruhn, Andrés; Grewenig, Sven; Böse, Katharina; Kraegeloh, Annette; Weickert, Joachim

    2013-12-01

    This paper proposes an advanced image enhancement method that is specifically tailored towards 3-D confocal and STED microscopy imagery. Our approach unifies image denoising, deblurring and interpolation in one joint method to handle the typical weaknesses of these advanced microscopy techniques: out-of-focus blur, Poisson noise and low axial resolution. In detail, we propose the combination of (i) Richardson-Lucy deconvolution, (ii) image restoration and (iii) anisotropic inpainting in one single scheme. To this end, we develop a novel PDE-based model that realizes these three ideas. First we consider a basic variational image restoration functional that is turned into a joint interpolation scheme by extending the regularization domain. Next, we integrate the variational representation of Richardson-Lucy deconvolution into our model, and illustrate its relation to Poisson distributed noise. In the following step, we supplement the components of our model with sub-quadratic penalization strategies that increase the robustness of the overall method. Finally, we consider the associated minimality conditions, where we exchange the occurring scalar-valued diffusivity function by a so-called diffusion tensor. This leads to an anisotropic regularization that is aligned with structures in the evolving image. As a further contribution of this paper, we propose a more efficient and faster semi-implicit iteration scheme that also increases the stability. Our experiments on real data sets demonstrate that this joint model achieves a superior reconstruction quality of the recorded cell.

  19. 3D printing of textile-based structures by Fused Deposition Modelling (FDM) with different polymer materials

    NASA Astrophysics Data System (ADS)

    Melnikova, R.; Ehrmann, A.; Finsterbusch, K.

    2014-08-01

    3D printing is a form of additive manufacturing, i.e. creating objects by sequential layering, for pre-production or production. After creating a 3D model with a CAD program, a printable file is used to create a layer design which is printed afterwards. While often more expensive than traditional techniques like injection moulding, 3D printing can significantly enhance production times of small parts produced in small numbers, additionally allowing for large flexibility and the possibility to create parts that would be impossible to produce with conventional techniques. The Fused Deposition Modelling technique uses a plastic filament which is pushed through a heated extrusion nozzle melting the material. Depending on the material, different challenges occur in the production process, and the produced part shows different mechanical properties. The article describes some standard and novel materials and their influence on the resulting parts.

  20. Comparison of 2D and 3D Fourier modal methods for modeling subwavelength-structured silicon waveguides

    NASA Astrophysics Data System (ADS)

    Kwiecien, Pavel; Richter, Ivan; Čtyroký, Jiří

    2012-02-01

    Frequency-domain Fourier modal methods have recently evolved into efficient tools for rigorous numerical modeling of a wide class of photonic and plasmonic structures and devices. In this contribution we describe the application of our 2D and 3D in-house tools, namely aperiodic rigorous coupled wave analysis (aRCWA) and bi-directional mode expansion propagation method using harmonic expansion (BEXX), on a recently described novel type of subwavelength grating (SWG) waveguides. They are created by means of periodically interlacing silicon segments with a superstrate material with a lower refractive index. It has been shown recently, both theoretically and experimentally, that for a suitable choice of SWG parameters such as grating period and duty cycle, the structure can support low-loss guided (Bloch) mode. Its effective index, mode profile and dispersion characteristics can thus be tailored to specific needs without the necessity of changing material composition. In our methods, either complex coordinate transformation or uniaxial anisotropic perfectly matched layers have been applied as efficient absorption boundary conditions. In order to reduce the number of expansion terms needed to reach required accuracy, the adaptive spatial resolution technique has been implemented. Structural symmetries of the devices can be fully utilized to this aim, too. Propagation constants of Bloch modes are also compared with those obtained with a full-vector film mode matching (FiMM) mode solver using the very simple effective medium theory (EMT).

  1. Comparison of 2D and 3D Fourier modal methods for modeling subwavelength-structured silicon waveguides

    NASA Astrophysics Data System (ADS)

    Kwiecien, Pavel; Richter, Ivan; Čtyroký, Jiří

    2011-09-01

    Frequency-domain Fourier modal methods have recently evolved into efficient tools for rigorous numerical modeling of a wide class of photonic and plasmonic structures and devices. In this contribution we describe the application of our 2D and 3D in-house tools, namely aperiodic rigorous coupled wave analysis (aRCWA) and bi-directional mode expansion propagation method using harmonic expansion (BEXX), on a recently described novel type of subwavelength grating (SWG) waveguides. They are created by means of periodically interlacing silicon segments with a superstrate material with a lower refractive index. It has been shown recently, both theoretically and experimentally, that for a suitable choice of SWG parameters such as grating period and duty cycle, the structure can support low-loss guided (Bloch) mode. Its effective index, mode profile and dispersion characteristics can thus be tailored to specific needs without the necessity of changing material composition. In our methods, either complex coordinate transformation or uniaxial anisotropic perfectly matched layers have been applied as efficient absorption boundary conditions. In order to reduce the number of expansion terms needed to reach required accuracy, the adaptive spatial resolution technique has been implemented. Structural symmetries of the devices can be fully utilized to this aim, too. Propagation constants of Bloch modes are also compared with those obtained with a full-vector film mode matching (FiMM) mode solver using the very simple effective medium theory (EMT).

  2. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-10-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry in Costa Rica is presented based on 3-D density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. Contrary to commonly assumed, to the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a maximum depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth (> 75 km) intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  3. BEAMS3D Neutral Beam Injection Model

    SciTech Connect

    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.

  4. Modeling Cellular Processes in 3-D

    PubMed Central

    Mogilner, Alex; Odde, David

    2011-01-01

    Summary Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated, we must address the issue of modeling cellular processes in 3-D. Here, we highlight recent advances related to 3-D modeling in cell biology. While some processes require full 3-D analysis, we suggest that others are more naturally described in 2-D or 1-D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3-D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling. PMID:22036197

  5. Fluid–Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure

    SciTech Connect

    Toma, Milan; Jensen, Morten Ø.; Einstein, Daniel R.; Yoganathan, Ajit P.; Cochran, Richard P.; Kunzelman, Karyn S.

    2015-07-17

    Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in-vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with *CT. Experimental data from the in-vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed lea et dynamics, and force vectors from the in-vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements are important in validating and adjusting material parameters in computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

  6. Fluid-Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure.

    PubMed

    Toma, Milan; Jensen, Morten Ø; Einstein, Daniel R; Yoganathan, Ajit P; Cochran, Richard P; Kunzelman, Karyn S

    2016-04-01

    Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with [Formula: see text]CT. Experimental data from the in vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed leaflet dynamics, and force vectors from the in vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements enable validating and adjusting material parameters to improve the accuracy of computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices. PMID:26183963

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  8. Radiosity diffusion model in 3D

    NASA Astrophysics Data System (ADS)

    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.

  9. Evaluation of 3D-Jury on CASP7 models

    PubMed Central

    Kaján, László; Rychlewski, Leszek

    2007-01-01

    Background 3D-Jury, the structure prediction consensus method publicly available in the Meta Server , was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. Results The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. Conclusion The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature available in the Meta Server. PMID:17711571

  10. Reservoir geology using 3D modelling tools

    SciTech Connect

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

    1996-12-31

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

  11. Reservoir geology using 3D modelling tools

    SciTech Connect

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

    1996-01-01

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

  12. Structural analysis of 3D high-speed train-bridge interactions for simple train load models

    NASA Astrophysics Data System (ADS)

    Lee, Yong-Seon; Kim, Sang-Hyo

    2010-02-01

    Three-dimensional models are developed for analysing the dynamic interaction that occurs between high-speed trains and bridges. The reliability and accuracy of developed models are verified by comparing the results from analysing field tests on high-speed trains. A number of train load models are proposed and their performances are compared in order to identify possible models that would reduce the computational and modelling efforts while maintaining suitable accuracy. The results show that at least 16 cars out of a 20-car train should be modelled to achieve results that are comparable to those obtained using the highly detailed 20-car model. Regarding the simplified train load model, more accurate results are obtained employing the 3D moving vehicle model for power cars, the heaviest cars of a high-speed trainset, and a moving force model for other cars, power passenger cars, and passenger cars, compared with highly detailed 20-car model.

  13. Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

    PubMed

    Halim, Sobia Ahsan; Zaheer-ul-Haq

    2015-08-01

    Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity. PMID:26051521

  14. Lithological 3D grid model of the Vuonos area built by using geostatistical simulation honoring the 3D fault model and structural trends of the Outokumpu association rocks in Eastern Finland

    NASA Astrophysics Data System (ADS)

    Laine, Eevaliisa

    2015-04-01

    The Outokumpu mining district - a metallogenic province about 100 km long x 60 km wide - hosts a Palaeoproterozoic sulfide deposit characterized by an unusual lithological association. It is located in the North Karelia Schist Belt , which was thrust on the late Archaean gneissic-granitoid basement of the Karelian craton during the early stages of the Svecofennian Orogeny between 1.92 and 1.87 Ga (Koistinen 1981). Two major tectono-stratigraphic units can be distinguished, a lower, parautochthonous 'Lower Kaleva' unit and an upper, allochthonous 'upper Kaleva' unit or 'Outokumpu allochthon'. The latter consists of tightly-folded deep marine turbiditic mica schists and metagraywackes containing intercalations of black schist, and the Outo¬kumpu assemblage, which comprises ca. 1950 Ma old, serpentinized peridotites surrounded by carbonate-calc-silicate ('skarn')-quartz rocks. The ore body is enclosed in the Outokumpu assemblage, which is thought to be part of a disrupted and incomplete ophiolite complex (Vuollo & Piirainen 1989) that can be traced to the Kainuu schist belt further north where the well-preserved Jormua ophiolite is ex¬posed (Kontinen 1987, Peltonen & Kontinen 2004). Outokumpu can be divided into blocks divided by faults and shear zones (Saalmann and Laine, 2014). The aim of this study was to make a 3D lithological model of a small part of the Outokumpu association rocks in the Vuonos area honoring the 3D fault model built by Saalmann and Laine (2014). The Vuonos study area is also a part of the Outokumpu mining camp area (Aatos et al. 2013, 2014). Fault and shear structures was used in geostatistical gridding and simulation of the lithologies. Several possible realizations of the structural grids, conforming the main lithological trends were built. Accordingly, it was possible to build a 3D structural grid containing information of the distribution of the possible lithologies and an estimation the associated uncertainties. References: Aatos, S

  15. Modeling and validation of a 3D velocity structure for the Santa Clara Valley, California, for seismic-wave simulations

    USGS Publications Warehouse

    Hartzell, S.; Harmsen, S.; Williams, R.A.; Carver, D.; Frankel, A.; Choy, G.; Liu, P.-C.; Jachens, R.C.; Brocher, T.M.; Wentworth, C.M.

    2006-01-01

    A 3D seismic velocity and attenuation model is developed for Santa Clara Valley, California, and its surrounding uplands to predict ground motions from scenario earthquakes. The model is developed using a variety of geologic and geophysical data. Our starting point is a 3D geologic model developed primarily from geologic mapping and gravity and magnetic surveys. An initial velocity model is constructed by using seismic velocities from boreholes, reflection/refraction lines, and spatial autocorrelation microtremor surveys. This model is further refined and the seismic attenuation is estimated through waveform modeling of weak motions from small local events and strong-ground motion from the 1989 Loma Prieta earthquake. Waveforms are calculated to an upper frequency of 1 Hz using a parallelized finite-difference code that utilizes two regions with a factor of 3 difference in grid spacing to reduce memory requirements. Cenozoic basins trap and strongly amplify ground motions. This effect is particularly strong in the Evergreen Basin on the northeastern side of the Santa Clara Valley, where the steeply dipping Silver Creek fault forms the southwestern boundary of the basin. In comparison, the Cupertino Basin on the southwestern side of the valley has a more moderate response, which is attributed to a greater age and velocity of the Cenozoic fill. Surface waves play a major role in the ground motion of sedimentary basins, and they are seen to strongly develop along the western margins of the Santa Clara Valley for our simulation of the Loma Prieta earthquake.

  16. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches.

    PubMed

    Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

    2015-08-01

    Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors. PMID:26194852

  17. 3D structure and nuclear targets

    NASA Astrophysics Data System (ADS)

    Dupré, Raphaël; Scopetta, Sergio

    2016-06-01

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

  18. Evolution of the Northeast German Basin — inferences from a 3D structural model and subsidence analysis

    NASA Astrophysics Data System (ADS)

    Scheck, M.; Bayer, U.

    1999-11-01

    A 3D structural model of the Northeast German Basin was evaluated with special emphasis on its evolution as an intracontinental depression. The study includes investigations on subsidence history and structural setting of the basin. Thickness evolution and calculated tectonic subsidence volumes of Permian to Quaternary sediments in the Northeast German Basin indicate that the subsidence history was related to five stages of basin evolution which differ in their subsidence mechanisms. For the initial rift phase in the Late Carboniferous to Early Permian, a dominant thermal event and subordinate horizontal stresses were indicated by thickness variation evolution and by structural evidence. The main part of basin subsidence occurred in a NW-SE-oriented basin in the subsequent phase of thermal relaxation with maximum subsidence from Early Permian (Rotliegend) to Middle Triassic (Muschelkalk). From Middle Triassic the thermal subsidence pattern was superposed by further tectonic events. In the Middle Triassic regional extension led to a reconfiguration of the southern part of the basin, where new NNE-SSW-trending troughs (Rheinsberg and Gifhorn Troughs) developed. In the Jurassic the northwestern part of the basin was uplifted while in the south the Keuper subsiding areas continued to sink and NW-SE-trending depressions, related to salt margins, became important. Differentiation continued into Cretaceous times when regional compression caused uplift of the southeastern part of the basin and basin margins. A final subsidence phase occurred in the Cenozoic. This was accompanied by intensive salt movement. Recent basin configuration reflects the superposition of structural elements resulting from different evolution stages. The main structural characteristics of the basin are: (1) a vertical tectonic zonation in a pre-Zechstein succession, which lacks significant internal structures, and a strongly deformed post-Zechstein succession, which was decoupled due to the thick

  19. Visualization of 3D Geological Models on Google Earth

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  20. BEAMS3D Neutral Beam Injection Model

    NASA Astrophysics Data System (ADS)

    McMillan, Matthew; Lazerson, Samuel A.

    2014-09-01

    With the advent of applied 3D fields 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 slowing down, and pitch angle scattering are modeled with the ADAS atomic physics database. Elementary benchmark calculations are presented to verify the collisionless particle orbits, NBI 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. Notice: this manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  1. Unravelling internal structures of an alkaline and carbonatite igneous complex by 3D modelling of gravity and magnetic data

    NASA Astrophysics Data System (ADS)

    Andersson, Magnus; Malehmir, Alireza

    2015-04-01

    Alnö igneous complex in central Sweden is among the few rare and largest alkaline and carbonatite ring-shaped intrusions in the world. Recent high-resolution reflection seismic profiles (Andersson et al., 2013) suggest a saucer-shaped magma chamber at about 3 km depth. Study of anisotropy of magnetic susceptibility (AMS) from a number of carbonatite dykes in the complex suggests a combination of laminar magma flow and sheet closure in the waning stage of magma transport for their emplacement (Andersson et al., 2015). Since 2010 and in conjunction with the above-mentioned studies, more than 400 gravity data points have been measured on land and partly on sea-ice. In addition, the Geological Survey of Sweden (SGU) provided about 100 data points. Petrophysical measurements including density and bulk magnetic susceptibility were carried out for more than 250 rock samples; magnetic remanence was measured on 39 of those samples. The measurements for example indicate that induced magnetisation is dominant in the complex and only a few rock samples show high remanent magnetisation (Q ≥ 1). SGU also provided airborne magnetic data (60 m flight altitude and 200 m flight line spacing) covering the complex on land and areas around it in the sea. These data show the complex as (i) a strong positive Bouguer anomaly, around 20 mGal, one of the strongest gravity gradients observed in Sweden, and (ii) a strong positive magnetic anomaly, around 2400 nT, additionally showing clear magnetic structures within the complex and adjacent to it in the sea. 3D inversion of the gravity and magnetic data was then performed using 100 m by 100 m meshes in the lateral direction and vertically varying meshes starting from 10 m at surface and increasing to 100 m in the depth interval 4250 - 8250 m. The inversion models cover an area of 17 km by 18 km. Regional fields were removed using a first-order polynomial surface for the gravity data and a constant (IGRF) for the magnetic data. Background

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

    PubMed Central

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

    2009-01-01

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

  3. Crust Uppermost Mantle Structure beneath Eastern Asia: Progress towards a Uniform, Tightly Constrained, High Resolution 3-D Model

    NASA Astrophysics Data System (ADS)

    Shen, W.; Ritzwoller, M. H.; Zheng, Y.; Lin, F. C.; Kim, Y.; Ning, J.; Kang, D.; Feng, L.; Wiens, D. A.

    2015-12-01

    In the past decade, large and dense seismic arrays have been deployed across much of eastern Asia (e.g., the "CEArray" and the "China Array" deployed by the China Earthquake Administration (CEA), the NECESS Array deployed collaboratively by China, Japan and the US, Korean Seismic Network, KNET and other networks in Japan, and historical PASSCAL installations), which have been used to produce increasingly well resolved models of the crust and uppermost mantle at different length scales. These models, however, do not cover eastern Asia uniformly. In this presentation, we report on an effort to generate a uniform high resolution 3-D model of the crust and uppermost mantle beneath eastern Asia using state-of-art surface wave and body wave inversion techniques. Highlights of this effort include: 1) We collect ambient noise cross-correlations using more than 1,800 seismic stations from multiple seismic arrays in this area and perform uniform surface wave tomography for the study area. 2) We collect P-wave receiver functions for over 1,000 stations and Rayleigh wave H/V ratio measurements for over 200 stations in this area. 3) We adopt a Bayesian Monte Carlo inversion to the Rayleigh wave dispersion maps and produce a uniform 3-D model with uncertainties of the crust and uppermost mantle. 4) In the areas where receiver functions and/or Rayleigh wave H/V ratios are collected, we replace the surface wave inversion by a joint inversion of surface waves and these seismic observables. The resulting model displays a great variety and considerable richness of geological and tectonic features in the crust and in the uppermost mantle which we summarize and discuss with focus on the relationship between the observed crustal variations and tectonic/geological boundaries and lithospheric modifications associated with volcanism in Northeast China.

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

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

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

  5. 3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing

    PubMed Central

    Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin

    2015-01-01

    Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein. PMID:25860348

  6. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing.

    PubMed

    Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin

    2015-01-01

    Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1). This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein. PMID:25860348

  7. 3-D Teaching Models for All

    ERIC Educational Resources Information Center

    Bradley, Joan; Farland-Smith, Donna

    2010-01-01

    Allowing a student to "see" through touch what other students see through a microscope can be a challenging task. Therefore, author Joan Bradley created three-dimensional (3-D) models with one student's visual impairment in mind. They are meant to benefit all students and can be used to teach common high school biology topics, including the…

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

    PubMed

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

    2013-07-01

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

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

    PubMed Central

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

    2013-01-01

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

  10. The 3D model of the lipase/acyltransferase from Candida parapsilosis, a tool for the elucidation of structural determinants in CAL-A lipase superfamily.

    PubMed

    Subileau, Maeva; Jan, Anne-Hélène; Nozac'h, Hervé; Pérez-Gordo, Marina; Perrier, Véronique; Dubreucq, Eric

    2015-10-01

    Because lipids are hydrophobic, the development of efficient bioconversions in aqueous media free of organic solvents is particularly challenging for green oleochemistry. Within this aim, enzymes exhibiting various abilities to catalyze acyltransfer reaction in water/lipid systems have been identified. Among these, CpLIP2 from Candida parapsilosis has been characterized as a lipase/acyltransferase, able to catalyze acyltransfer reactions preferentially to hydrolysis in the presence of particularly low acyl acceptor concentration and high thermodynamic activity of water (aw>0.9). Lipase/acyltransferases are thus of great interest, being able to produce new esters at concentrations above the thermodynamic equilibrium of hydrolysis/esterification with limited to no release of free fatty acids. Here, we present a 3D model of CpLIP2 based on homologies with crystallographic structures of Pseudozyma antarctica lipase A. Indeed, the two enzymes have 31% of identity in their primary sequence, yielding a same general structure, but different catalytic properties. The quality of the calculated CpLIP2 model was confirmed by several methods. Limited proteolysis confirmed the location of some loops at the surface of the protein 3D model. Directed mutagenesis also supported the structural model constructed on CAL-A template: the functional properties of various mutants were consistent with their structure-based putative involvement in the oxyanion hole, substrate specificity, acyltransfer or hydrolysis catalysis and structural stability. The CpLIP2 3D model, in comparison with CAL-A 3D structure, brings insights for the elucidation and improvement of the structural determinants involved in the exceptional acyltransferase properties of this promising biocatalyst and of homologous enzymes of the same family. PMID:26123263

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

    PubMed

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

    2008-01-01

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

  12. Debris Dispersion Model Using Java 3D

    NASA Technical Reports Server (NTRS)

    Thirumalainambi, Rajkumar; Bardina, Jorge

    2004-01-01

    This paper describes web based simulation of Shuttle launch operations and debris dispersion. Java 3D graphics provides geometric and visual content with suitable mathematical model and behaviors of Shuttle launch. Because the model is so heterogeneous and interrelated with various factors, 3D graphics combined with physical models provides mechanisms to understand the complexity of launch and range operations. The main focus in the modeling and simulation covers orbital dynamics and range safety. Range safety areas include destruct limit lines, telemetry and tracking and population risk near range. If there is an explosion of Shuttle during launch, debris dispersion is explained. The shuttle launch and range operations in this paper are discussed based on the operations from Kennedy Space Center, Florida, USA.

  13. 3-D electromagnetic modeling of wakefields in accelerator components

    SciTech Connect

    Poole, B.R.; Caporaso, G.J.; Ng, Wang C.; Shang, C.C.; Steich, D.

    1996-09-18

    We discuss the use of 3-D finite-difference time-domain (FDTD) electromagnetic codes for modeling accelerator components. Computational modeling of cylindrically symmetric structures such as induction accelerator cells has been very successful in predicting the wake potential and wake impedances of these structures, but full 3-D modeling of complex structures has been limited due to substantial computer resources required for a full 3-D model. New massively parallel 3-D time domain electromagnetic codes now under development using conforming unstructured meshes allow a substantial increase in the geometric fidelity of the structures being modeled. Development of these new codes are discussed in context of applicability to accelerator problems. Various 3-D structures are tested with an existing cubical cell FDTD code and wake impedances compared with simple analytic models for the structures; results will be used as benchmarks for testing the new time time domain codes. Structures under consideration include a stripline beam position monitor as well as circular and elliptical apertures in circular waveguides. Excellent agreement for monopole and dipole impedances with models were found for these structures below the cutoff frequency of the beam line.

  14. 3-D electromagnetic modeling of wakefields in accelerator components

    SciTech Connect

    Poole, Brian R.; Caporaso, George J.; Ng, Wang C.; Shang, Clifford C.; Steich, David

    1997-02-01

    We discuss the use of 3-D finite-difference time-domain (FDTD) electromagnetic codes for the modeling of accelerator components. Computational modeling of cylindrically symmetric structures such as induction accelerator cells has been extremely successful in predicting the wake potential and wake impedances of these structures, but fully 3-D modeling of complex structures has been limited due to the substantial computer resources required for a fully 3-D model. New massively parallel 3-D time domain electromagnetic codes now under development using conforming unstructured meshes allow a substantial increase in the geometric fidelity of the structures being modeled. Development of these new codes will be discussed in the context of their applicability to accelerator problems. A variety of 3-D structures are tested with an existing cubical cell FDTD code and the wake impedances are compared with simple analytic models for the structures. These results will provide a set of benchmarks for testing the new time domain codes. Structures under consideration include a stripline beam position monitor as well as circular and elliptical apertures in circular waveguides. Excellent agreement for the monopole and dipole impedances with the models are found for these structures below the cutoff frequency of the beam line.

  15. Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.

    PubMed

    Lee, Sehan; Barron, Mace G

    2015-11-01

    Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs. PMID:26202430

  16. 3D Ultrasonic Wave Simulations for Structural Health Monitoring

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  17. 3D Structure of Tillage Soils

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    PubMed Central

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

    2010-01-01

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

  19. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

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

  20. Illustrative visualization of 3D city models

    NASA Astrophysics Data System (ADS)

    Doellner, Juergen; Buchholz, Henrik; Nienhaus, Marc; Kirsch, Florian

    2005-03-01

    This paper presents an illustrative visualization technique that provides expressive representations of large-scale 3D city models, inspired by the tradition of artistic and cartographic visualizations typically found in bird"s-eye view and panoramic maps. We define a collection of city model components and a real-time multi-pass rendering algorithm that achieves comprehensible, abstract 3D city model depictions based on edge enhancement, color-based and shadow-based depth cues, and procedural facade texturing. Illustrative visualization provides an effective visual interface to urban spatial information and associated thematic information complementing visual interfaces based on the Virtual Reality paradigm, offering a huge potential for graphics design. Primary application areas include city and landscape planning, cartoon worlds in computer games, and tourist information systems.

  1. 3D gravity modeling of a salt structure associated to the Trozza-Labaied lineament (Central Tunisia) constrained by seismic and borehole data

    NASA Astrophysics Data System (ADS)

    Djebbi, M.; Gabtni, H.

    2015-03-01

    Gravity and seismic are two distinctive geophysical methods which are used combined in integrated geophysical studies. The rationale behind this integration is to construct a 3D gravity model for a salt structure associated to the Trozza-Labaied major tectonic deformation. The Trozza-Labaied area witnessed the occurrence of several tectonic events during the Atlassic phase resulting in the creation of various salt structures. Interpretation of the available seismic data revealed the different lithological units forming the geologic setting. Whereas the analysis of the gravity data contributed in exposing the existence of different gravity anomalies. Thus, the integrated seismic and gravity data are fundamental in constructing a 3D gravity model. The resulting model provides an accurate image of the salt body extent and its geometry and determines its effect over the surrounding sedimentary deposits.

  2. NoSQL Based 3D City Model Management System

    NASA Astrophysics Data System (ADS)

    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.

  3. Sensing and compressing 3-D models

    SciTech Connect

    Krumm, J.

    1998-02-01

    The goal of this research project was to create a passive and robust computer vision system for producing 3-D computer models of arbitrary scenes. Although the authors were unsuccessful in achieving the overall goal, several components of this research have shown significant potential. Of particular interest is the application of parametric eigenspace methods for planar pose measurement of partially occluded objects in gray-level images. The techniques presented provide a simple, accurate, and robust solution to the planar pose measurement problem. In addition, the representational efficiency of eigenspace methods used with gray-level features were successfully extended to binary features, which are less sensitive to illumination changes. The results of this research are presented in two papers that were written during the course of this project. The papers are included in sections 2 and 3. The first section of this report summarizes the 3-D modeling efforts.

  4. In vivo trp scanning of the small multidrug resistance protein EmrE confirms 3D structure models'.

    PubMed

    Lloris-Garcerá, Pilar; Slusky, Joanna S G; Seppälä, Susanna; Prieß, Marten; Schäfer, Lars V; von Heijne, Gunnar

    2013-11-15

    The quaternary structure of the homodimeric small multidrug resistance protein EmrE has been studied intensely over the past decade. Structural models derived from both two- and three-dimensional crystals show EmrE as an anti-parallel homodimer. However, the resolution of the structures is rather low and their relevance for the in vivo situation has been questioned. Here, we have challenged the available structural models by a comprehensive in vivo Trp scanning of all four transmembrane helices in EmrE. The results are in close agreement with the degree of lipid exposure of individual residues predicted from coarse-grained molecular dynamics simulations of the anti-parallel dimeric structure obtained by X-ray crystallography, strongly suggesting that the X-ray structure provides a good representation of the active in vivo form of EmrE. PMID:23920359

  5. Analyses of Magnetic Structures of Active Region 11117 Evolution using a 3D Data-Driven Magnetohydrodynamic Model

    NASA Astrophysics Data System (ADS)

    Wu, Shi; Jiang, Chaowei; Feng, Xueshang

    We use the photospheric vector magnetograms obtained by Helioseismic and Magnetic Image (HMI) on-board the Solar Dynamic Observatory (SDO) as the boundary conditions for a Data-Driven CESE-MHD model (Jiang et al. 2012) to investigate the physical characteristics and evolution of magnetic field configurations in the corona before and after a solar eruptive event. Specifically, the evolution of AR11117 characteristics such as length of magnetic shear along the neutral line, current helicity, magnetic free energy and the energy flux across the photosphere due to flux emergence and surface flow are presented. The computed 3D magnetic field configuration are compared with AIA (Atmosphere Image Assembly) which shows remarkable resemblance. A topological analyses reveals that the small flare is correlated with a bald patch (BP, where the magnetic field is tangent to the photosphere), suggesting that the energy release of the flare is caused by magnetic reconnection associated with the BP separatrices. The total magnetic flux and energy keep increasing slightly in spite of flare, while the computed magnetic free energy drops during the flare by 10 (30) ergs which is adequate in providing the energy budget of a minor C-class confined flare as observed. Jiang, Chaowei, Xueshang, Feng, S. T Wu and Qiang Hu, Ap. J., 759:85, 2012 Nov 10

  6. Beyond textbook illustrations: Hand-held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers.

    PubMed

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-11-01

    Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported. PMID:21567863

  7. Robust hashing for 3D models

    NASA Astrophysics Data System (ADS)

    Berchtold, Waldemar; Schäfer, Marcel; Rettig, Michael; Steinebach, Martin

    2014-02-01

    3D models and applications are of utmost interest in both science and industry. With the increment of their usage, their number and thereby the challenge to correctly identify them increases. Content identification is commonly done by cryptographic hashes. However, they fail as a solution in application scenarios such as computer aided design (CAD), scientific visualization or video games, because even the smallest alteration of the 3D model, e.g. conversion or compression operations, massively changes the cryptographic hash as well. Therefore, this work presents a robust hashing algorithm for 3D mesh data. The algorithm applies several different bit extraction methods. They are built to resist desired alterations of the model as well as malicious attacks intending to prevent correct allocation. The different bit extraction methods are tested against each other and, as far as possible, the hashing algorithm is compared to the state of the art. The parameters tested are robustness, security and runtime performance as well as False Acceptance Rate (FAR) and False Rejection Rate (FRR), also the probability calculation of hash collision is included. The introduced hashing algorithm is kept adaptive e.g. in hash length, to serve as a proper tool for all applications in practice.

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

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

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

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

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

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

  10. Gis-Based Smart Cartography Using 3d Modeling

    NASA Astrophysics Data System (ADS)

    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.

  11. Fallon FORGE 3D Geologic Model

    DOE Data Explorer

    Doug Blankenship

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Haas, Kevin A.; Warner, John C.

    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.

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

    USGS Publications Warehouse

    Haas, K.A.; Warner, J.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. ?? 2008 Elsevier Ltd.

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Evaluation of Structure from Motion Software to Create 3D Models of Late Nineteenth Century Great Lakes Shipwrecks Using Archived Diver-Acquired Video Surveys

    NASA Astrophysics Data System (ADS)

    Mertes, J.; Thomsen, T.; Gulley, J.

    2014-12-01

    Here we demonstrate the ability to use archived video surveys to create photorealistic 3D models of submerged archeological sites. We created 3D models of two nineteenth century Great Lakes shipwrecks using diver-acquired video surveys and Structure from Motion (SfM) software. Models were georeferenced using archived hand survey data. Comparison of hand survey measurements and digital measurements made using the models demonstrate that spatial analysis produces results with reasonable accuracy when wreck maps are available. Error associated with digital measurements displayed an inverse relationship to object size. Measurement error ranged from a maximum of 18 % (on 0.37 m object) and a minimum of 0.56 % (on a 4.21 m object). Our results demonstrate SfM can generate models of large maritime archaeological sites that for research, education and outreach purposes. Where site maps are available, these 3D models can be georeferenced to allow additional spatial analysis long after on-site data collection.

  17. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups

    ERIC Educational Resources Information Center

    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…

  18. Free Tools and Strategies for the Generation of 3D Finite Element Meshes: Modeling of the Cardiac Structures

    PubMed Central

    Pavarino, E.; Neves, L. A.; Machado, J. M.; de Godoy, M. F.; Shiyou, Y.; Momente, J. C.; Zafalon, G. F. D.; Pinto, A. R.; Valêncio, C. R.

    2013-01-01

    The Finite Element Method is a well-known technique, being extensively applied in different areas. Studies using the Finite Element Method (FEM) are targeted to improve cardiac ablation procedures. For such simulations, the finite element meshes should consider the size and histological features of the target structures. However, it is possible to verify that some methods or tools used to generate meshes of human body structures are still limited, due to nondetailed models, nontrivial preprocessing, or mainly limitation in the use condition. In this paper, alternatives are demonstrated to solid modeling and automatic generation of highly refined tetrahedral meshes, with quality compatible with other studies focused on mesh generation. The innovations presented here are strategies to integrate Open Source Software (OSS). The chosen techniques and strategies are presented and discussed, considering cardiac structures as a first application context. PMID:23762031

  19. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

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

    2015-07-15

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

  20. Molecular cloning and 3D structure modeling of APEX1, DNA base excision repair enzyme from the Camel, Camelus dromedarius.

    PubMed

    Ataya, Farid Shokry; Fouad, Dalia; Malik, Ajamaluddin; Saeed, Hesham Mahmoud

    2012-01-01

    The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%-97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939. PMID:22942721

  1. 3D Model of Surfactant Replacement Therapy

    NASA Astrophysics Data System (ADS)

    Grotberg, James; Tai, Cheng-Feng; Filoche, Marcel

    2015-11-01

    Surfactant Replacement Therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. Though successful in neonatal applications, its use in adults had early success followed by failure. We present the first mathematical model of 3D SRT where a liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug first deposits a coating film on the airway wall which subtracts from its volume, a ``coating cost''. Then the plug splits unevenly at the airway bifurcation due to gravity. The steps are repeated until a plug ruptures or reaches the tree endpoint alveoli/acinus. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published literature, the earlier successful adult SRT studies show comparatively good index values, while the later failed studies do not. Those unsuccessful studies used smaller dose volumes with higher concentration mixtures, apparently assuming a well mixed compartment. The model shows that adult lungs are not well mixed in SRT due to the coating cost and gravity effects. Returning to the higher dose volume protocols could save many thousands of lives annually in the US. Supported by NIH Grants HL85156, HL84370 and Agence Nationale de la Recherche, ANR no. 2010-BLAN-1119-05.

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

    PubMed Central

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

    2015-01-01

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

  3. A right-lateral structural model for Poui Field, offshore Trinidad, from 3D seismic interpretation and subsurface well control

    SciTech Connect

    Wolfe, J.E.; Sobol, F.T. )

    1993-02-01

    A new wrench fault structural model is developed for Poui Field, in the Colombus Basin, offshore Trinidad. A strain ellipse for a right-lateral simple shear stress field is demonstrated from observed fault patterns on recent seismic mapping of deep hydrocarbon-bearing sands at Poui Field. The seismic interpretation is calibrated by 20 points of well control which penetrated the best, continuous, mappable reflector at these deep sand levels. Seismic cross-sections taken over the Poui structure, which are perpendicular to the structural axis of the feature, and constrained by well control, demonstrate geometries typical of wrench faulting observed along the Los Bajos fault complex, onshore Trinidad, and along the San Andreas wrench fault systems of southern California. Variable dip rate along the fault, flower structures with associated sag features, asymmetry of the structure, an extensional duplex, and a possible horsetail splay appear on the maps and cross-sections, and support the wrench fault model. Various pieces of subsurface information, observed in the Field from well control, support the wrench hypothesis: isolated, pressure separated compartments, abrupt facies changes across faults and hydrocarbon migration anomalies. Subsequent extensional faulting created an overprinting of rotated, normal faulting that followed fracture planes created by the right-lateral simple shear stress field. Regional mapping indicates that this wrench fault is a stress field. Regional mapping indicates that this wrench fault is a continuation of the right-lateral fault system mapped onshore Trinidad as the Marcel Main fault system.

  4. MOSSFRAC: An anisotropic 3D fracture model

    SciTech Connect

    Moss, W C; Levatin, J L

    2006-08-14

    Despite the intense effort for nearly half a century to construct detailed numerical models of plastic flow and plastic damage accumulation, models for describing fracture, an equally important damage mechanism still cannot describe basic fracture phenomena. Typical fracture models set the stress tensor to zero for tensile fracture and set the deviatoric stress tensor to zero for compressive fracture. One consequence is that the simple case of the tensile fracture of a cylinder under combined compressive radial and tensile axial loads is not modeled correctly. The experimental result is a cylinder that can support compressive radial loads, but no axial load, whereas, the typical numerical result is a cylinder with all stresses equal to zero. This incorrect modeling of fracture locally also has a global effect, because material that is fracturing produces stress release waves, which propagate from the fracture and influence the surrounding material. Consequently, it would be useful to have a model that can describe the stress relief and the resulting anisotropy due to fracture. MOSSFRAC is a material model that simulates three-dimensional tensile and shear fracture in initially isotropic elastic-plastic materials, although its framework is also amenable to initially anisotropic materials. It differs from other models by accounting for the effects of cracks on the constitutive response of the material, so that the previously described experiment, as well as complicated fracture scenarios are simulated more accurately. The model is implemented currently in the LLNL hydrocodes DYNA3D, PARADYN, and ALE3D. The purpose of this technical note is to present a complete qualitative description of the model and quantitative descriptions of salient features.

  5. Estimating the subsurface temperature of Hessen/Germany based on a GOCAD 3D structural model - a comparison of numerical and geostatistical approaches

    NASA Astrophysics Data System (ADS)

    Rühaak, W.; Bär, K.; Sass, I.

    2012-04-01

    Based on a 3D structural GOCAD model of the German federal state Hessen the subsurface temperature distribution is computed. Since subsurface temperature data for greater depth are typically sparse, two different approaches for estimating the spatial subsurface temperature distribution are tested. One approach is the numerical computation of a 3D purely conductive steady state temperature distribution. This numerical model is based on measured thermal conductivity data for all relevant geological units, together with heat flow measurements and surface temperatures. The model is calibrated using continuous temperature-logs. Here only conductive heat transfer is considered as data for convective heat transport at great depth are currently not available. The other approach is by 3D ordinary Kriging; applying a modified approach where the quality of the temperature measurements is taken into account. A difficult but important part here is to derive good variograms for the horizontal and vertical direction. The variograms give necessary information about the spatial dependence. Both approaches are compared and discussed. Differences are mainly related due to convective processes, which are reflected by the interpolation result, but not by the numerical model. Therefore, a comparison of the two results is a good way to obtain information about flow processes in such great depth. This way an improved understanding of this mid enthalpy geothermal reservoir (1000 - 6000 m) is possible. Future work will be the reduction of the small but - especially for depth up to approximately 1000 m - relevant paleoclimate signal.

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    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

  8. 3D Stratigraphic Modeling of Central Aachen

    NASA Astrophysics Data System (ADS)

    Dong, M.; Neukum, C.; Azzam, R.; Hu, H.

    2010-05-01

    Since 1980s, advanced computer hardware and software technologies, as well as multidisciplinary research have provided possibilities to develop advanced three dimensional (3D) simulation software for geosciences application. Some countries, such as USA1) and Canada2) 3), have built up regional 3D geological models based on archival geological data. Such models have played huge roles in engineering geology2), hydrogeology2) 3), geothermal industry1) and so on. In cooperating with the Municipality of Aachen, the Department of Engineering Geology of RWTH Aachen University have built up a computer-based 3D stratigraphic model of 50 meter' depth for the center of Aachen, which is a 5 km by 7 km geologically complex area. The uncorrelated data from multi-resources, discontinuous nature and unconformable connection of the units are main challenges for geological modeling in this area. The reliability of 3D geological models largely depends on the quality and quantity of data. Existing 1D and 2D geological data were collected, including 1) approximately 6970 borehole data of different depth compiled in Microsoft Access database and MapInfo database; 2) a Digital Elevation Model (DEM); 3) geological cross sections; and 4) stratigraphic maps in 1m, 2m and 5m depth. Since acquired data are of variable origins, they were managed step by step. The main processes are described below: 1) Typing errors of borehole data were identified and the corrected data were exported to Variowin2.2 to distinguish duplicate points; 2) The surface elevation of borehole data was compared to the DEM, and differences larger than 3m were eliminated. Moreover, where elevation data missed, it was read from the DEM; 3) Considerable data were collected from municipal constructions, such as residential buildings, factories, and roads. Therefore, many boreholes are spatially clustered, and only one or two representative points were picked out in such areas; After above procedures, 5839 boreholes with -x

  9. Density structure and geometry of the Costa Rican subduction zone from 3-D gravity modeling and local earthquake data

    NASA Astrophysics Data System (ADS)

    Lücke, O. H.; Arroyo, I. G.

    2015-07-01

    The eastern part of the oceanic Cocos Plate presents a heterogeneous crustal structure due to diverse origins and ages as well as plate-hot spot interactions which originated the Cocos Ridge, a structure that converges with the Caribbean Plate in southeastern Costa Rica. The complex structure of the oceanic plate directly influences the dynamics and geometry of the subduction zone along the Middle American Trench. In this paper an integrated interpretation of the slab geometry is presented based on three-dimensional density modeling of combined satellite and surface gravity data, constrained by available geophysical and geological data and seismological information obtained from local networks. The results show the continuation of steep subduction geometry from the Nicaraguan margin into Northwestern Costa Rica, followed by a moderate dipping slab under the Central Cordillera toward the end of the Central American Volcanic Arc. To the southeast end of the volcanic arc, our preferred model shows a steep, coherent slab that extends up to the landward projection of the Panama Fracture Zone. Overall, a gradual change in the depth of the intraplate seismicity is observed, reaching 220 km in the northwestern part, and becoming progressively shallower toward the southeast, where it reaches a terminal depth of 75 km. The changes in the terminal depth of the observed seismicity correlate with the increased density in the modeled slab. The absence of intermediate depth intraplate seismicity in the southeastern section and the higher densities for the subducted slab in this area, support a model in which dehydration reactions in the subducted slab cease at a shallower depth, originating an anhydrous and thus aseismic slab.

  10. An approach for the 3D dynamic mathematical modelization of big structures with special respect to Ariane 5

    NASA Astrophysics Data System (ADS)

    Dieker, S.

    1993-10-01

    With special respect to Ariane 5, solutions are outlined that allow an improvement of the mathematical modeling and calculation in structural dynamics. Substructuring, and the application of modern component mode synthesis methods, are necessary. However, most of the methods result in modal degrees of freedom (DOF) of the interfaces and demand a high effort to couple the substructures. A general method is described that overcomes the disadvantages of the modal interface DOFs. As a result, the coupling of substructures is reduced to a simple addition of matrices. All reduced matrices of the substructures are real and symmetric. In a second section, special aspects of modeling are discussed. Structural aspects that are taken into account are the viscoelastic material behavior of the propellant of the solid rocket booster, the idealization of fluids and shells, and the fluid-structure-interaction. The coupling between axial, lateral and circumferential wave modes of Ariane 5 is no longer negligible; a hybrid description of the DOFs of the complete launcher by grid point displacements and Fourier series is possible, and offers an additional way to reduce the number of DOFs.

  11. An approach for the 3D dynamic mathematical modelization of big structures with special respect to ARIANE 5

    NASA Astrophysics Data System (ADS)

    Dieker, S.

    With special respect to ARIANE 5, solutions are outlined that allow an improvement of the mathematical modelization and calculation in structural dynamics. Substructuring and the application of modern component mode synthesis methods (e.g. Craig-Chang) are necessary. However, most of the methods result in modal degrees of freedom (DOF) of the interfaces and demand a high effort to couple the substructures. In this paper, a general method is described that allows to overcome the disadvantages of the modal interface DOFs. As a result, the coupling of substructures is reduced to a simple addition of matrices. The methods of Craig-Chang and Hurty resp. Craig-Bampton are special applications of this method. All reduced matrices of the substructures are real and symmetric. In a second section, special aspects of modelization are discussed. Structural aspects that are taken into accout are the viscoelastic material behaviour of the propellant of the solid rocket booster, the idealization of fluids and shells and the fluid-structure-interaction including the stiffening effect of the tank pressure. Finally, the coupling between axial, lateral and circumferential wave modes of the launcher ARIANE 5 is no longer neglectable. The mathematical representation of the interfaces between adjacent substructures is of some importance. A hybrid description of the DOFs of the complete launcher by grid point displacements and Fourier series is possible and offers an additional way to reduce the number of DOFs.

  12. Waveform Modeling of 3D Structure of D" Region Using A Coupled SEM/Normal Mode Approach

    NASA Astrophysics Data System (ADS)

    To, A.; Gung, Y.; Capadeville, Y.; Romanowicz, B.

    2003-12-01

    The presence of strong lateral heterogeneity in D" is now well documented and presents challenges for seismic modeling. The main challenges are the limited global sampling of D" and the theoretical limits of validity of the present modeling tools, such as standard ray theory and mode approaches. We use coupled normal mode/Spectral Element Method (SEM) to compute synthetic seismograms of Sdiff in the D" part of a tomographic model(SAW24b16, Mégnin and Romanowicz, 2000) down to corner frequency 1/12s. SEM allows to take into account strong heterogeneity in a rigorous manner. The coupled method is much faster than standard SEM, when the numerical part of the computation is restricted to the D" region. In the rest of the mantle, the wave field is computed using efficient normal mode summation. As a first step, we consider a radially symmetric model outside of the D" region, and compare Sdiff synthetics with observed waveforms for a collection of deep earthquakes, for which the effect of strong heterogeneity in the crust and upper mantle is avoided. Observed and synthetic travel time trends are very consistent and in many cases the observed residuals are significantly larger. This indicates that the tomographic model only represents the smooth features of the real structure. Observed waveform amplitudes and SEM synthetics are somewhat less consistent. We compare the predictions for 800 Sdiff phases using SEM with those obtained by more approximate methods : ray theory and NACT (Non-linear asymptotic coupling theory, a normal mode perturbation approach). We discuss systematic trends in the travel times predicted by the different methods, compared to observations. Starting with the tomographic model, and correcting for mantle structure outside of D" using approximate NACT predictions, we next invert for perturbations to the tomographic model, using the coupled SEM/mode computation for the forward part of the modeling, in several regions of D" under the Pacific, which are

  13. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    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

  15. Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

    PubMed Central

    Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

    2014-01-01

    Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. Impact of soil structure heterogeneity on the degradation of organic pollutants at the centimeter scale : 3D Modeling using graph based method

    NASA Astrophysics Data System (ADS)

    Sinclair Yemini, Francis; Chenu, Claire; Monga, Olivier; Vieuble Gonond, Laure; Juarez, Sabrina; Pihneiro, Marc; otten, Wilfred; Garnier, Patricia

    2014-05-01

    Contaminant degradation by microorganisms is very variable in soils because of the very heterogeneous spatial relationship of contaminant/degraders. Repacked Soil columns were carried out to study the degradation of 2,4D pesticide labelled with C14 for different scenarios of microorganisms and pesticide initial location. Measurements of global C14-CO2 emission and C14 distribution in the soil column showed that the initial location play a crucial rule on the dissipation of the pollutant. Experiments were simulated using a 3D model able to model microbial degradation and substrate diffusion between aggregates by considering explicitly the 3D structure of soil from CT images. The initial version of the model (Monga et al., 2008) was improved in order to simulate diffusion in samples of large size. Partial differential equations were implemented using freefem++ solver. The model simulates properly the dynamics of 2,4D in the column for the different initial situations. CT images of the same soil but using undisturbed structure instead of repacked aggregates were also carried out. Significant differences of the simulated results were observed between the repacked and the undisturbed soil. The conclusion of our work is that the heterogeneity of the soil structure and location of pollutants and decomposers has a very strong influence on the dissipation of pollutants.

  19. 3D Modeling of Equatorial Plasma Bubbles

    NASA Astrophysics Data System (ADS)

    Huba, Joseph; Joyce, Glenn; Krall, Jonathan

    2011-10-01

    Post-sunset ionospheric irregularities in the equatorial F region were first observed by Booker and Wells (1938) using ionosondes. This phenomenon has become known as equatorial spread F (ESF). During ESF the equatorial ionosphere becomes unstable because of a Rayleigh-Taylor-like instability: large scale (10s km) electron density ``bubbles'' can develop and rise to high altitudes (1000 km or greater at times). Understanding and modeling ESF is important because of its impact on space weather: it causes radio wave scintillation that degrades communication and navigation systems. In fact, it is the focus of of the Air Force Communications/Navigation Outage Forecast Satellite (C/NOFS) mission. We will describe 3D simulation results from the NRL ionosphere models SAMI3 and SAMI3/ESF of this phenomenon. In particular, we will examine the causes of the day-to-day ariability of ESF which is an unresolved problem at this time. Post-sunset ionospheric irregularities in the equatorial F region were first observed by Booker and Wells (1938) using ionosondes. This phenomenon has become known as equatorial spread F (ESF). During ESF the equatorial ionosphere becomes unstable because of a Rayleigh-Taylor-like instability: large scale (10s km) electron density ``bubbles'' can develop and rise to high altitudes (1000 km or greater at times). Understanding and modeling ESF is important because of its impact on space weather: it causes radio wave scintillation that degrades communication and navigation systems. In fact, it is the focus of of the Air Force Communications/Navigation Outage Forecast Satellite (C/NOFS) mission. We will describe 3D simulation results from the NRL ionosphere models SAMI3 and SAMI3/ESF of this phenomenon. In particular, we will examine the causes of the day-to-day ariability of ESF which is an unresolved problem at this time. Research supported by ONR.

  20. A time series generalized functional model based method for vibration-based damage precise localization in structures consisting of 1D, 2D, and 3D elements

    NASA Astrophysics Data System (ADS)

    Sakaris, C. S.; Sakellariou, J. S.; Fassois, S. D.

    2016-06-01

    This study focuses on the problem of vibration-based damage precise localization via data-based, time series type, methods for structures consisting of 1D, 2D, or 3D elements. A Generalized Functional Model Based method is postulated based on an expanded Vector-dependent Functionally Pooled ARX (VFP-ARX) model form, capable of accounting for an arbitrary structural topology. The FP model's operating parameter vector elements are properly constrained to reflect any given topology. Damage localization is based on operating parameter vector estimation within the specified topology, so that the location estimate and its uncertainty bounds are statistically optimal. The method's effectiveness is experimentally demonstrated through damage precise localization on a laboratory spatial truss structure using various damage scenarios and a single pair of random excitation - vibration response signals in a low and limited frequency bandwidth.

  1. Beyond Textbook Illustrations: Hand-Held Models of Ordered DNA and Protein Structures as 3D Supplements to Enhance Student Learning of Helical Biopolymers

    ERIC Educational Resources Information Center

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2010-01-01

    Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we…

  2. STELLOPT Modeling of the 3D Diagnostic Response in ITER

    SciTech Connect

    Lazerson, Samuel A

    2013-05-07

    The ITER three dimensional diagnostic response to an n=3 resonant magnetic perturbation is modeled using the STELLOPT code. The in-vessel coils apply a resonant magnetic perturbation (RMP) fi eld which generates a 4 cm edge displacement from axisymmetry as modeled by the VMEC 3D equilibrium code. Forward modeling of flux loop and magnetic probe response with the DIAGNO code indicates up to 20 % changes in measured plasma signals. Simulated LIDAR measurements of electron temperature indicate 2 cm shifts on the low field side of the plasma. This suggests that the ITER diagnostic will be able to diagnose the 3D structure of the equilibria.

  3. Patient-specific geometrical modeling of orthopedic structures with high efficiency and accuracy for finite element modeling and 3D printing.

    PubMed

    Huang, Huajun; Xiang, Chunling; Zeng, Canjun; Ouyang, Hanbin; Wong, Kelvin Kian Loong; Huang, Wenhua

    2015-12-01

    We improved the geometrical modeling procedure for fast and accurate reconstruction of orthopedic structures. This procedure consists of medical image segmentation, three-dimensional geometrical reconstruction, and assignment of material properties. The patient-specific orthopedic structures reconstructed by this improved procedure can be used in the virtual surgical planning, 3D printing of real orthopedic structures and finite element analysis. A conventional modeling consists of: image segmentation, geometrical reconstruction, mesh generation, and assignment of material properties. The present study modified the conventional method to enhance software operating procedures. Patient's CT images of different bones were acquired and subsequently reconstructed to give models. The reconstruction procedures were three-dimensional image segmentation, modification of the edge length and quantity of meshes, and the assignment of material properties according to the intensity of gravy value. We compared the performance of our procedures to the conventional procedures modeling in terms of software operating time, success rate and mesh quality. Our proposed framework has the following improvements in the geometrical modeling: (1) processing time: (femur: 87.16 ± 5.90 %; pelvis: 80.16 ± 7.67 %; thoracic vertebra: 17.81 ± 4.36 %; P < 0.05); (2) least volume reduction (femur: 0.26 ± 0.06 %; pelvis: 0.70 ± 0.47, thoracic vertebra: 3.70 ± 1.75 %; P < 0.01) and (3) mesh quality in terms of aspect ratio (femur: 8.00 ± 7.38 %; pelvis: 17.70 ± 9.82 %; thoracic vertebra: 13.93 ± 9.79 %; P < 0.05) and maximum angle (femur: 4.90 ± 5.28 %; pelvis: 17.20 ± 19.29 %; thoracic vertebra: 3.86 ± 3.82 %; P < 0.05). Our proposed patient-specific geometrical modeling requires less operating time and workload, but the orthopedic structures were generated at a higher rate of success as compared with the conventional method. It is expected to benefit the surgical planning of orthopedic

  4. 3D Structure of Sulfolobus solfataricus Carboxypeptidase Developed by Molecular Modeling is Confirmed by Site-Directed Mutagenesis and Small Angle X-Ray Scattering

    PubMed Central

    Occhipinti, Emanuela; Martelli, Pier Luigi; Spinozzi, Francesco; Corsi, Federica; Formantici, Cristina; Molteni, Laura; Amenitsch, Heintz; Mariani, Paolo; Tortora, Paolo; Casadio, Rita

    2003-01-01

    Sulfolobus solfataricus carboxypeptidase (CPSso) is a thermostable zinc-metalloenzyme with a Mr of 43,000. Taking into account the experimentally determined zinc content of one ion per subunit, we developed two alternative 3D models, starting from the available structures of Thermoactinomyces vulgaris carboxypeptidase (Model A) and Pseudomonas carboxypeptidase G2 (Model B). The former enzyme is monomeric and has one metal ion in the active site, while the latter is dimeric and has two bound zinc ions. The two models were computed by exploiting the structural alignment of the one zinc- with the two zinc-containing active sites of the two templates, and with a threading procedure. Both computed structures resembled the respective template, with only one bound zinc with tetrahedric coordination in the active site. With these models, two different quaternary structures can be modeled: one using Model A with a hexameric symmetry, the other from Model B with a tetrameric symmetry. Mutagenesis experiments directed toward the residues putatively involved in metal chelation in either of the models disproved Model A and supported Model B, in which the metal-binding site comprises His108, Asp109, and His168. We also identified Glu142 as the acidic residue interacting with the water molecule occupying the fourth chelation site. Furthermore, the overall fold and the oligomeric structure of the molecule was validated by small angle x-ray scattering (SAXS). An ab initio original approach was used to reconstruct the shape of the CPSso in solution from the experimental curves. The results clearly support a tetrameric structure. The Monte Carlo method was then used to compare the crystallographic coordinates of the possible quaternary structures for CPSso with the SAXS profiles. The fitting procedure showed that only the model built using the Pseudomonas carboxypeptidase G2 structure as a template fitted the experimental data. PMID:12885660

  5. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    2013-06-23

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

  6. Multivariate 3D modelling of Scottish soil properties

    NASA Astrophysics Data System (ADS)

    Poggio, Laura; Gimona, Alessandro

    2015-04-01

    Information regarding soil properties across landscapes at national or continental scales is critical for better soil and environmental management and for climate regulation and adaptation policy. The prediction of soil properties variation in space and time and their uncertainty is an important part of environmental modelling. Soil properties, and in particular the 3 fractions of soil texture, exhibit strong co-variation among themselves and therefore taking into account this correlation leads to spatially more accurate results. In this study the continuous vertical and lateral distributions of relevant soil properties in Scottish soils were modelled with a multivariate 3D-GAM+GS approach. The approach used involves 1) modelling the multivariate trend with full 3D spatial correlation, i.e., exploiting the values of the neighbouring pixels in 3D-space, and 2) 3D kriging to interpolate the residuals. The values at each cell for each of the considered depth layers were defined using a hybrid GAM-geostatistical 3D model, combining the fitting of a GAM (generalised Additive Models) to estimate multivariate trend of the variables, using a 3D smoother with related covariates. Gaussian simulations of the model residuals were used as spatial component to account for local details. A dataset of about 26,000 horizons (7,800 profiles) was used for this study. A validation set was randomly selected as 25% of the full dataset. Numerous covariates derived from globally available data, such as MODIS and SRTM, are considered. The results of the 3D-GAM+kriging showed low RMSE values, good R squared and an accurate reproduction of the spatial structure of the data for a range of soil properties. The results have an out-of-sample RMSE between 10 to 15% of the observed range when taking into account the whole profile. The approach followed allows the assessment of the uncertainty of both the trend and the residuals.

  7. Regional geothermal 3D modelling in Denmark

    NASA Astrophysics Data System (ADS)

    Poulsen, S. E.; Balling, N.; Bording, T. S.; Nielsen, S. B.

    2012-04-01

    In the pursuit of sustainable and low carbon emission energy sources, increased global attention has been given to the exploration and exploitation of geothermal resources within recent decades. In 2009 a national multi-disciplinary geothermal research project was established. As a significant part of this project, 3D temperature modelling is to be carried out, with special emphasis on temperatures of potential geothermal reservoirs in the Danish area. The Danish subsurface encompasses low enthalpy geothermal reservoirs of mainly Triassic and Jurassic age. Geothermal plants at Amager (Copenhagen) and Thisted (Northern Jutland) have the capacity of supplying the district heating network with up to 14 MW and 7 MW, respectively, by withdrawing warm pore water from the Gassum (Lower Jurassic/Upper Triassic) and Bunter (Lower Triassic) sandstone reservoirs, respectively. Explorative studies of the subsurface temperature regime typically are based on a combination of observations and modelling. In this study, the open-source groundwater modelling code MODFLOW is modified to simulate the subsurface temperature distribution in three dimensions by taking advantage of the mathematical similarity between saturated groundwater flow (Darcy flow) and heat conduction. A numerical model of the subsurface geology in Denmark is built and parameterized from lithological information derived from joint interpretation of seismic surveys and borehole information. Boundary conditions are constructed from knowledge about the heat flow from the Earth's interior and the shallow ground temperature. Matrix thermal conductivities have been estimated from analysis of high-resolution temperature logs measured in deep wells and porosity-depth relations are included using interpreted main lithologies. The model takes into account the dependency of temperature and pressure on thermal conductivity. Moreover, a transient model based correction of the paleoclimatic thermal disturbance caused by the

  8. The Benefit of 3D Laser Scanning Technology in the Generation and Calibration of FEM Models for Health Assessment of Concrete Structures

    PubMed Central

    Yang, Hao; Xu, Xiangyang; Neumann, Ingo

    2014-01-01

    Terrestrial laser scanning technology (TLS) is a new technique for quickly getting three-dimensional information. In this paper we research the health assessment of concrete structures with a Finite Element Method (FEM) model based on TLS. The goal focuses on the benefits of 3D TLS in the generation and calibration of FEM models, in order to build a convenient, efficient and intelligent model which can be widely used for the detection and assessment of bridges, buildings, subways and other objects. After comparing the finite element simulation with surface-based measurement data from TLS, the FEM model is determined to be acceptable with an error of less than 5%. The benefit of TLS lies mainly in the possibility of a surface-based validation of results predicted by the FEM model. PMID:25414968

  9. 3D visualization of middle ear structures

    NASA Astrophysics Data System (ADS)

    Vogel, Uwe; Schmitt, Thomas

    1998-06-01

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

  10. Identification of the Structural Features of Guanine Derivatives as MGMT Inhibitors Using 3D-QSAR Modeling Combined with Molecular Docking.

    PubMed

    Sun, Guohui; Fan, Tengjiao; Zhang, Na; Ren, Ting; Zhao, Lijiao; Zhong, Rugang

    2016-01-01

    DNA repair enzyme O⁶-methylguanine-DNA methyltransferase (MGMT), which plays an important role in inducing drug resistance against alkylating agents that modify the O⁶ position of guanine in DNA, is an attractive target for anti-tumor chemotherapy. A series of MGMT inhibitors have been synthesized over the past decades to improve the chemotherapeutic effects of O⁶-alkylating agents. In the present study, we performed a three-dimensional quantitative structure activity relationship (3D-QSAR) study on 97 guanine derivatives as MGMT inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Three different alignment methods (ligand-based, DFT optimization-based and docking-based alignment) were employed to develop reliable 3D-QSAR models. Statistical parameters derived from the models using the above three alignment methods showed that the ligand-based CoMFA (Qcv² = 0.672 and Rncv² = 0.997) and CoMSIA (Qcv² = 0.703 and Rncv² = 0.946) models were better than the other two alignment methods-based CoMFA and CoMSIA models. The two ligand-based models were further confirmed by an external test-set validation and a Y-randomization examination. The ligand-based CoMFA model (Qext² = 0.691, Rpred² = 0.738 and slope k = 0.91) was observed with acceptable external test-set validation values rather than the CoMSIA model (Qext² = 0.307, Rpred² = 0.4 and slope k = 0.719). Docking studies were carried out to predict the binding modes of the inhibitors with MGMT. The results indicated that the obtained binding interactions were consistent with the 3D contour maps. Overall, the combined results of the 3D-QSAR and the docking obtained in this study provide an insight into the understanding of the interactions between guanine derivatives and MGMT protein, which will assist in designing novel MGMT inhibitors with desired activity. PMID:27347909

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

    PubMed

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

    2014-09-23

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

  12. 3-D ore body modeling and structural settings of syn-to late orogenic Variscan hydrothermal mineralization, Siegerland district, Rhenish Massif, NW Germany

    NASA Astrophysics Data System (ADS)

    Peters, Meike; Hellmann, André; Meyer, Franz Michael

    2013-04-01

    The Siegerland district is located in the fold-and thrust-belt of the Rhenish Massif and hosts diverse syn-to late orogenic mineralization styles. Peak-metamorphism and deformation occurred at 312-316±10 Ma (Ahrendt et al., 1978) at temperature-pressure conditions of 280-320°C and 0.7-1.4 kbar (Hein, 1993). In addition to syn-orogenic siderite-quartz mineralization at least four different syn-to late orogenic mineralization stages are identified comprising Co-Ni-Cu-Au, Pb-Zn-Cu, Sb-Au, and hematite-digenite-bornite ores (Hellmann et al., 2012). The earliest type of syn-orogenic ore mineralization is formed by siderite-quartz veins, trending N-S, E-W and NE-SW. The vein systems are closely related to fold and reverse fault geometries (Hellmann et al., 2012). The most important structural feature is the first-order Siegen main reverse fault showing an offset into three major faults (Peters et al., 2012). The structural control on ore formation is demonstrated by the Co-Ni-Cu-Au mineralization generally hosted by NE-ENE trending reverse faults and associated imbrication zones that have reactivated the older siderite-quartz veins. In this study, we developed a 3-D model of the Alte Buntekuh ore bodies in the Siegerland district, using Datamine Studio3 to investigate the structural setting of Co-Ni-Cu-Au mineralization. The salient structural and spatial data for the 3-D model were taken from old mine level plans as well as from geological and topographical maps. The ore bodies are located immediately in the hanging wall of the southern branch of the Siegen main reverse fault (Peters et al., 2012). From the model it becomes obvious, that the earlier siderite-quartz veins, dipping steeply to the NW, are cross-cut and segmented by oppositely dipping oblique reverse faults. Individual ore body segments are rotated and displaced, showing a plunge direction to the SW. The 3-D model further reveals the presence of hook-like, folded vein arrays, highly enriched in cobalt

  13. Potential of 3D City Models to assess flood vulnerability

    NASA Astrophysics Data System (ADS)

    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

  14. Creating Physical 3D Stereolithograph Models of Brain and Skull

    PubMed Central

    Kelley, Daniel J.; Farhoud, Mohammed; Meyerand, M. Elizabeth; Nelson, David L.; Ramirez, Lincoln F.; Dempsey, Robert J.; Wolf, Alan J.; Alexander, Andrew L.; Davidson, Richard J.

    2007-01-01

    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. PMID:17971879

  15. 3-D physical models of amitosis (cytokinesis).

    PubMed

    Cheng, Kang; Zou, Changhua

    2005-01-01

    Based on Newton's laws, extended Coulomb's law and published biological data, we develop our 3-D physical models of natural and normal amitosis (cytokinesis), for prokaryotes (bacterial cells) in M phase. We propose following hypotheses: Chromosome rings exclusion: No normally and naturally replicated chromosome rings (RCR) can occupy the same prokaryote, a bacterial cell. The RCR produce spontaneous and strong electromagnetic fields (EMF), that can be alternated environmentally, in protoplasm and cortex. The EMF is approximately a repulsive quasi-static electric (slowly variant and mostly electric) field (EF). The EF forces between the RCR are strong enough, and orderly accumulate contractile proteins that divide the procaryotes in the cell cortex of division plane or directly split the cell compartment envelope longitudinally. The radial component of the EF forces could also make furrows or cleavages of procaryotes. The EF distribution controls the protoplasm partition and completes the amitosis (cytokinesis). After the cytokinesis, the spontaneous and strong EF disappear because the net charge accumulation becomes weak, in the protoplasm. The exclusion is because the two sets of informative objects (RCR) have identical DNA codes information and they are electro magnetically identical, therefore they repulse from each other. We also compare divisions among eukaryotes, prokaryotes, mitochondria and chloroplasts and propose our hypothesis: The principles of our models are applied to divisions of mitochondria and chloroplasts of eucaryotes too because these division mechanisms are closer than others in a view of physics. Though we develop our model using 1 division plane (i.e., 1 cell is divided into 2 cells) as an example, the principle of our model is applied to the cases with multiple division planes (i.e., 1 cell is divided into multiple cells) too. PMID:15533619

  16. 3D Models of Stellar Interactions

    NASA Astrophysics Data System (ADS)

    Mohamed, S.; Podsiadlowski, Ph.; Booth, R.; Maercker, M.; Ramstedt, S.; Vlemmings, W.; Harries, T.; Mackey, J.; Langer, N.; Corradi, R.

    2014-04-01

    Symbiotic binaries consist of a cool, evolved mass-losing giant and an accreting compact companion. As symbiotic nebulae show similar morphologies to those in planetary nebulae (so much so that it is often difficult to distinguish between the two), they are ideal laboratories for understanding the role a binary companion plays in shaping the circumstellar envelopes in these evolved systems. We will present 3D Smoothed Particle Hydrodynamics (SPH) models of interacting binaries, e.g. R Aquarii and Mira, and discuss the formation of spiral outflows, arcs, shells and equatorial density enhancements.We will also discuss the implications of the former for planetary nebulae, e.g. the Egg Nebula and Cat's Eye, and the latter for the formation of bipolar geometries, e.g. M2-9. We also investigate accretion and angular momentum evolution in symbiotic binaries which may be important to understand the formation of jets and more episodic mass-loss features we see in circumstellar envelopes and the orbital characteristics of binary central stars of planetary nebulae.

  17. Multi-view and 3D deformable part models.

    PubMed

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

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ). PMID:26440264

  18. 3D Geological Model for "LUSI" - a Deep Geothermal System

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

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

    2012-07-01

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

  20. Teaching the geological subsurface with 3D models

    NASA Astrophysics Data System (ADS)

    Thorpe, Steve; Ward, Emma

    2014-05-01

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

  1. Object-oriented urban 3D spatial data model organization method

    NASA Astrophysics Data System (ADS)

    Li, Jing-wen; Li, Wen-qing; Lv, Nan; Su, Tao

    2015-12-01

    This paper combined the 3d data model with object-oriented organization method, put forward the model of 3d data based on object-oriented method, implemented the city 3d model to quickly build logical semantic expression and model, solved the city 3d spatial information representation problem of the same location with multiple property and the same property with multiple locations, designed the space object structure of point, line, polygon, body for city of 3d spatial database, and provided a new thought and method for the city 3d GIS model and organization management.

  2. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

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

    2010-01-01

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

  3. Modeling of mass and charge transport in a solid oxide fuel cell anode structure by a 3D lattice Boltzmann approach

    NASA Astrophysics Data System (ADS)

    Paradis, Hedvig; Andersson, Martin; Sundén, Bengt

    2015-09-01

    A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.

  4. Modeling of mass and charge transport in a solid oxide fuel cell anode structure by a 3D lattice Boltzmann approach

    NASA Astrophysics Data System (ADS)

    Paradis, Hedvig; Andersson, Martin; Sundén, Bengt

    2016-08-01

    A 3D model at microscale by the lattice Boltzmann method (LBM) is proposed for part of an anode of a solid oxide fuel cell (SOFC) to analyze the interaction between the transport and reaction processes and structural parameters. The equations of charge, momentum, heat and mass transport are simulated in the model. The modeling geometry is created with randomly placed spheres to resemble the part of the anode structure close to the electrolyte. The electrochemical reaction processes are captured at specific sites where spheres representing Ni and YSZ materials are present with void space. This work focuses on analyzing the effect of structural parameters such as porosity, and percentage of active reaction sites on the ionic current density and concentration of H2 using LBM. It is shown that LBM can be used to simulate an SOFC anode at microscale and evaluate the effect of structural parameters on the transport processes to improve the performance of the SOFC anode. It was found that increasing the porosity from 30 to 50 % decreased the ionic current density due to a reduction in the number of reaction sites. Also the consumption of H2 decreased with increasing porosity. When the percentage of active reaction sites was increased while the porosity was kept constant, the ionic current density increased. However, the H2 concentration was slightly reduced when the percentage of active reaction sites was increased. The gas flow tortuosity decreased with increasing porosity.

  5. Acoustic 3D imaging of dental structures

    SciTech Connect

    Lewis, D.K.; Hume, W.R.; Douglass, G.D.

    1997-02-01

    Our goals for the first year of this three dimensional electodynamic imaging project was to determine how to combine flexible, individual addressable; preprocessing of array source signals; spectral extrapolation or received signals; acoustic tomography codes; and acoustic propagation modeling code. We investigated flexible, individually addressable acoustic array material to find the best match in power, sensitivity and cost and settled on PVDF sheet arrays and 3-1 composite material.

  6. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  7. A biochemical/biophysical 3D FE intervertebral disc model.

    PubMed

    Schroeder, Y; Huyghe, J M; van Donkelaar, C C; Ito, K

    2010-10-01

    Present research focuses on different strategies to preserve the degenerated disc. To assure long-term success of novel approaches, favorable mechanical conditions in the disc tissue are essential. To evaluate these, a model is required that can determine internal mechanical conditions which cannot be directly measured as a function of assessable biophysical characteristics. Therefore, the objective is to evaluate if constitutive and material laws acquired on isolated samples of nucleus and annulus tissue can be used directly in a whole-organ 3D FE model to describe intervertebral disc behavior. The 3D osmo-poro-visco-hyper-elastic disc (OVED) model describes disc behavior as a function of annulus and nucleus tissue biochemical composition, organization and specific constituent properties. The description of the 3D collagen network was enhanced to account for smaller fibril structures. Tissue mechanical behavior tests on isolated nucleus and annulus samples were simulated with models incorporating tissue composition to calculate the constituent parameter values. The obtained constitutive laws were incorporated into the whole-organ model. The overall behavior and disc properties of the model were corroborated against in vitro creep experiments of human L4/L5 discs. The OVED model simulated isolated tissue experiments on confined compression and uniaxial tensile test and whole-organ disc behavior. This was possible, provided that secondary fiber structures were accounted for. The fair agreement (radial bulge, axial creep deformation and intradiscal pressure) between model and experiment was obtained using constitutive properties that are the same for annulus and nucleus. Both tissue models differed in the 3D OVED model only by composition. The composition-based modeling presents the advantage of reducing the numbers of material parameters to a minimum and to use tissue composition directly as input. Hence, this approach provides the possibility to describe internal

  8. A 3-D shape model of Interamnia

    NASA Astrophysics Data System (ADS)

    Sato, Isao

    2015-08-01

    A 3-D shape model of the sixth largest of the main belt asteroids, (704) Interamnia, is presented. The model is reproduced from its two stellar occultation observations and six lightcurves between 1969 and 2011. The first stellar occultation was the occultation of TYC 234500183 on 1996 December 17 observed from 13 sites in the USA. An elliptical cross section of (344.6±9.6km)×(306.2±9.1km), for position angle P=73.4±12.5 was fitted. The lightcurve around the occultation shows that the peak-to-peak amplitude was 0.04 mag. and the occultation phase was just before the minimum. The second stellar occultation was the occultation of HIP 036189 on 2003 March 23 observed from 39 sites in Japan and Hawaii. An elliptical cross section of (349.8±0.9km)×(303.7±1.7km), for position angle P=86.0±1.1 was fitted. A companion of 8.5 mag. of the occulted star was discovered whose separation is 12±2 mas (milli-arcseconds), P=148±11 . A combined analysis of rotational lightcurves and occultation chords can return more information than can be obtained with either technique alone. From follow-up photometric observations of the asteroid between 2003 and 2011, its rotation period is determined to be 8.728967167±0.00000007 hours, which is accurate enough to fix the rotation phases at other occultation events. The derived north pole is λ2000=259±8, β2000=-50±5 (retrograde rotation); the lengths of the three principal axes are 2a=361.8±2.8km, 2b=324.4±5.0km, 2c=297.3±3.5km, and the mean diameter is D=326.8±3.0km. Supposing the mass of Interamnia as (3.5±0.9)×10-11 solar masses, the density is then ρ=3.8±1.0 g cm-3.

  9. cyp51A-based mechanism of azole resistance in Aspergillus fumigatus: Illustration by a new 3D Structural Model of Aspergillus fumigatus CYP51A protein.

    PubMed

    Liu, Musang; Zheng, Nan; Li, Dongmei; Zheng, Hailin; Zhang, Lili; Ge, Hu; Liu, Weida

    2016-05-01

    Mutations of CYP51A protein (Cytochrome P450 14-α Sterol demethylase) play a central role in the azole resistance of Aspergillus fumigatus The available structural models of CYP51A protein ofA. fumigatus are built based on that of Homo sapiens and that of Mycobacterium tuberculosis, of which the amino acid homology is only 38% and 29% compared with CYP51A protein ofA. fumigatus, respectively. In the present study, we constructed a new 3D structural model ofA. fumigatus CYP51A protein based on a recently resolved crystal structure of the homologous protein in the fungus S. cerevisiae, which shares 50% amino acid homology with A. fumigatus CYP51A protein. Three azole molecules, itraconazole, voriconazole, and posaconazole, were docked to the wild-type and the mutant A. fumigatus CYP51A protein models, respectively, to illustrate the impact of cyp51A mutations to azole-resistance. We found the mutations that occurred at L98, M220, and Y431 positions would decrease the binding affinity of azoles to the CYP51A protein and therefore would reduce their inhibitory effects. Additionally, the mutations of L98 and G432 would reduce the stability of the protein, which might lead to conformational change of its binding pocket and eventually the resistance to azoles. PMID:26768370

  10. 3D geometric modelling of hand-woven textile

    NASA Astrophysics Data System (ADS)

    Shidanshidi, H.; Naghdy, F.; Naghdy, G.; Conroy, D. Wood

    2008-02-01

    Geometric modeling and haptic rendering of textile has attracted significant interest over the last decade. A haptic representation is created by adding the physical properties of an object to its geometric configuration. While research has been conducted into geometric modeling of fabric, current systems require time-consuming manual recognition of textile specifications and data entry. The development of a generic approach for construction of the 3D geometric model of a woven textile is pursued in this work. The geometric model would be superimposed by a haptic model in the future work. The focus at this stage is on hand-woven textile artifacts for display in museums. A fuzzy rule based algorithm is applied to the still images of the artifacts to generate the 3D model. The derived model is exported as a 3D VRML model of the textile for visual representation and haptic rendering. An overview of the approach is provided and the developed algorithm is described. The approach is validated by applying the algorithm to different textile samples and comparing the produced models with the actual structure and pattern of the samples.

  11. 3D Modeling Techniques for Print and Digital Media

    NASA Astrophysics Data System (ADS)

    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.

  12. Texture blending on 3D models using casual images

    NASA Astrophysics Data System (ADS)

    Liu, Xingming; Liu, Xiaoli; Li, Ameng; Liu, Junyao; Wang, Huijing

    2013-12-01

    In this paper, a method for constructing photorealistic textured model using 3D structured light digitizer is presented. Our method acquisition of range images and texture images around object, and range images are registered and integrated to construct geometric model of object. System is calibrated and poses of texture-camera are determined so that the relationship between texture and geometric model is established. After that, a global optimization is applied to assign compatible texture to adjacent surface and followed with a level procedure to remove artifacts due to vary lighting, approximate geometric model and so on. Lastly, we demonstrate the effect of our method on constructing a real model of world.

  13. 3D cartographic modeling of the Alpine arc

    NASA Astrophysics Data System (ADS)

    Vouillamoz, Naomi; Sue, Christian; Champagnac, Jean-Daniel; Calcagno, Philippe

    2012-12-01

    We built a 3D cartography of the Alpine arc, a highly non-cylindrical mountain belt, using the 3D GeoModeller of the BRGM (French geological survey). The model allows to handle the large-scale 3D structure of seventeen major crustal units of the belt (from the lower crust to the sedimentary cover nappes), and two main discontinuities (the Insubric Line and the Crustal Penninic Front). It provides a unique document to better understand their structural relationships and to produce new sections. The study area comprises the western Alpine arc, from the Jura to the Northwest, up to the Bergell granite intrusion and the Lepontine Dome to the East, and is limited to the South by the Ligurian basin. The model is limited vertically 10 km above sea level at the top, and the moho interface at the bottom. We discarded the structural relationships between the Alps sensus stricto and the surrounding geodynamic systems such as the Rhine graben or the connection with the Apennines. The 3D-model is based on the global integration of various data such as the DEM of the Alps, the moho isobaths, the simplified geological and tectonic maps of the belt, the crustal cross-sections ECORS-CROP and NFP-20, and complementary cross-sections specifically built to precise local complexities. The database has first been integrated in a GIS-project to prepare their implementation in the GeoModeller, by homogenizing the different spatial referencing systems. The global model is finally interpolated from all these data, using the potential field method. The final document is a new tri-dimensional cartography that would be used as input for further alpine studies.

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

    PubMed

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

    2008-07-01

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

  15. 3d model for site effect assessment at Nice (France)

    NASA Astrophysics Data System (ADS)

    Bertrand, E.; Courrioux, G.; Bourgine, B.; Bour, M.; Guillen, A.; Mouroux, P.; Devaux, E.; Duval, A. M.

    2003-04-01

    Assessment of lithologic site effects is based on an accurate knowledge of properties and geometry of superficial geological formations, i.e. ideally a 3D-4G subsurface model (Geology, Geomorphology, Geophysics, Geotechnics). Such a model has been achieved using a 3D geomodeler ("Geological Editor" developed at BRGM) that allows building 3D volumes of geological formations starting from drill-holes data, sections, and geological maps. This software uses a pseudo-stratigraphic pile in order to reproduce geological history and structural relationships (erosion, deposit). The interpolation is achieved through a 3D potential field. A geostatistical formulation allows to consider data points of a geological limit as equipotential, and sructural dips as gradient inputs for the 3D field interpolation. Then isosurfaces corresponding to each limit are combined using formation relationships to provide volumic models of geological formations. The first task was to identify the relevant geological formations underlying in Nice area. In a first approach Mesozoic bedrock, Pliocene bedrock, and Quaternary alluvial deposits have been distinguished considering their seismic properties. Then alluvions have been subdivided into 9 groups according to their lithology and granulometry. Modelling has been performed considering 2 major erosion surfaces, post-Mesozoic and post-Pliocene. The succession of Quaternary alluviums have been considered as "onlap deposits". Given adjacent lithologies contained in maps and drill holes, these relations lead to logical identification of the roof of formations to be interpolated. The distribution of modeled geological formations can be visualised in 3 dimensions or in 2D sections. Besides the visual interest of 3D representations, the model is first used to build a series of earth columns over a 50m/50m 2D grid. A statistical analysis allowed to identify 73 existing configurations in the Nice district area. Among these, only 15 configurations

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

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  18. 3D high resolution mineral phase distribution and seismic velocity structure of the transition zone: predicted by a full spherical-shell compressible mantle convection model

    NASA Astrophysics Data System (ADS)

    Geenen, T.; Heister, T.; Van Den Berg, A. P.; Jacobs, M.; Bangerth, W.

    2011-12-01

    We present high resolution 3D results of the complex mineral phase distribution in the transition zone obtained by numerical modelling of mantle convection. We extend the work by [Jacobs and van den Berg, 2011] to 3D and illustrate the efficiency of adaptive mesh refinement for capturing the complex spatial distribution and sharp phase transitions as predicted by their model. The underlying thermodynamical model is based on lattice dynamics which allows to predict thermophysical properties and seismic wave speeds for the applied magnesium-endmember olivine-pyroxene mineralogical model. The use of 3D geometry allows more realistic prediction of phase distribution and seismic wave speeds resulting from 3D flow processes involving the Earth's transition zone and more significant comparisons with interpretations from seismic tomography and seismic reflectivity studies aimed at the transition zone. Model results are generated with a recently developed geodynamics modeling application based on dealII (www.dealii.org). We extended this model to incorporate both a general thermodynamic model, represented by P,T space tabulated thermophysical properties, and a solution strategy that allows for compressible flow. When modeling compressible flow in the so called truncated anelastic approximation framework we have to adapt the solver strategy that has been proven by several authors to be highly efficient for incompressible flow to incorporate an extra term in the continuity equation. We present several possible solution strategies and discuss their implication in terms of robustness and computational efficiency.

  19. 3D modeling of metallic grain growth

    SciTech Connect

    George, D.; Carlson, N.; Gammel, J.T.; Kuprat, A.

    1999-06-01

    This paper will describe simulating metallic grain growth using the Gradient Weighted Moving Finite Elements code, GRAIN3D. The authors also describe the set of mesh topology change operations developed to respond to changes in the physical topology such as the collapse of grains and to maintain uniform calculational mesh quality. Validation of the method is demonstrated by comparison to analytic calculations. The authors present results of multigrain simulations where grain boundaries evolve by mean curvature motion and include results which incorporate grain boundary orientation dependence.

  20. The 3D rocket combustor acoustics model

    NASA Technical Reports Server (NTRS)

    Priem, Richard J.; Breisacher, Kevin J.

    1992-01-01

    The theory and procedures for determining the characteristics of pressure oscillations in rocket engines with prescribed burning rate oscillations are presented. Analyses including radial and hub baffles and absorbers can be performed in one, two, and three dimensions. Pressure and velocity oscillations calculated using this procedure are presented for the SSME to show the influence of baffles and absorbers on the burning rate oscillations required to achieve neutral stability. Comparisons are made between the results obtained utilizing 1-D, 2-D, and 3-D assumptions with regards to capturing the physical phenomena of interest and computational requirements.

  1. 3D Geological modelling - towards a European level infrastructure

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  2. Verification of a Flow3d Mathematical Model by a Physical Hydraulic Model of a Turbine Intake Structure of a Small Hydropower Plant and a Practical Use of the Mathematical Model

    NASA Astrophysics Data System (ADS)

    Vosnjak, S.; Mlacnik, J.

    2009-04-01

    The Drava Power Plants Utility company is the owner of all hydropower plants on the Drava River, Slovenia. On the flood waves relief structure of the Zlatoličje HPP headrace channel the construction of a turbine intake structure for the Melje small hydropower plant is planned. The Melje small HPP shall exploit the biological minimum discharge for electricity production. Since the structure shall be small, the price of a physical hydraulic model research, in comparison with the price of the structure itself, would be too high. Consequently, the client decided to test the designed structure in the cheapest possible way and ordered a 3D mathematical model of the turbine intake structure. By this mathematical model the designed form of the intake structure should be verified, or, in case of non-compliance, a modified form of such structure which would meet the required modes of the SHPP operation should be proposed. Since such a 3D mathematical model hasn't been used for a hydraulic modelling of this type yet, the project performers were slightly mistrustful of the results obtained by it. Regarding our long years' experiences with physical modelling we decided to construct also a physical hydraulic model in order to be able to verify the designed form of the intake structure and then to use the results for the 3D mathematical model calibration. A partial physical hydraulic model was constructed in the Laboratory for Hydraulic Research in Ljubljana in a model scale of 1:20. For construction and implementation of all the necessary research only 30 days were needed. Simultaneously with the physical model all the preparatory arrangements for the geometry of the mathematical model were going on. During the further development of the mathematical model, also some additional researches on the physical model were performed. Considering the time needed to fully establish the functionality of the mathematical model, it showed up to be very time consuming even in comparison to

  3. 3D model of the Bernese Part of the Swiss Molasse Basin: visualization of uncertainties in a 3D model

    NASA Astrophysics Data System (ADS)

    Mock, Samuel; Allenbach, Robin; Reynolds, Lance; Wehrens, Philip; Kurmann-Matzenauer, Eva; Kuhn, Pascal; Michael, Salomè; Di Tommaso, Gennaro; Herwegh, Marco

    2016-04-01

    The Swiss Molasse Basin comprises the western and central part of the North Alpine Foreland Basin. In recent years it has come under closer scrutiny due to its promising geopotentials such as geothermal energy and CO2 sequestration. In order to adress these topics good knowledge of the subsurface is a key prerequisite. For that matter, geological 3D models serve as valuable tools. In collaboration with the Swiss Geological Survey (swisstopo) and as part of the project GeoMol CH, a geological 3D model of the Swiss Molasse Basin in the Canton of Bern has been built. The model covers an area of 1810 km2and reaches depth of up to 6.7 km. It comprises 10 major Cenozoic and Mesozoic units and numerous faults. The 3D model is mainly based on 2D seismic data complemented by information from few deep wells. Additionally, data from geological maps and profiles were used for refinement at shallow depths. In total, 1163 km of reflection seismic data, along 77 seismic lines, have been interpreted by different authors with respect to stratigraphy and structures. Both, horizons and faults, have been interpreted in 2D and modelled in 3D using IHS's Kingdom Suite and Midland Valley's MOVE software packages, respectively. Given the variable degree of subsurface information available, each 3D model is subject of uncertainty. With the primary input data coming from interpretation of reflection seismic data, a variety of uncertainties comes into play. Some of them are difficult to address (e.g. author's style of interpretation) while others can be quantified (e.g. mis-tie correction, well-tie). An important source of uncertainties is the quality of seismic data; this affects the traceability and lateral continuation of seismic reflectors. By defining quality classes we can semi-quantify this source of uncertainty. In order to visualize the quality and density of the input data in a meaningful way, we introduce quality-weighted data density maps. In combination with the geological 3D

  4. Modelling Polymer Deformation during 3D Printing

    NASA Astrophysics Data System (ADS)

    McIlroy, Claire; Olmsted, Peter

    Three-dimensional printing has the potential to transform manufacturing processes, yet improving the strength of printed parts, to equal that of traditionally-manufactured parts, remains an underlying issue. The fused deposition modelling technique involves melting a thermoplastic, followed by layer-by-layer extrusion to fabricate an object. The key to ensuring strength at the weld between layers is successful inter-diffusion. However, prior to welding, both the extrusion process and the cooling temperature profile can significantly deform the polymer micro-structure and, consequently, how well the polymers are able to ``re-entangle'' across the weld. In particular, polymer alignment in the flow can cause de-bonding of the layers and create defects. We have developed a simple model of the non-isothermal extrusion process to explore the effects that typical printing conditions and material rheology have on the conformation of a polymer melt. In particular, we incorporate both stretch and orientation using the Rolie-Poly constitutive equation to examine the melt structure as it flows through the nozzle, the subsequent alignment with the build plate and the resulting deformation due to the fixed nozzle height, which is typically less than the nozzle radius.

  5. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

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

    2011-01-01

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

  6. Influence of pre-existing basement faults on the structural evolution of the Zagros Simply Folded belt: 3D numerical modelling

    NASA Astrophysics Data System (ADS)

    Ruh, Jonas B.; Gerya, Taras

    2015-04-01

    The Simply Folded Belt of the Zagros orogen is characterized by elongated fold trains symptomatically defining the geomorphology along this mountain range. The Zagros orogen results from the collision of the Arabian and the Eurasian plates. The Simply Folded Belt is located southwest of the Zagros suture zone. An up to 2 km thick salt horizon below the sedimentary sequence enables mechanical and structural detachment from the underlying Arabian basement. Nevertheless, deformation within the basement influences the structural evolution of the Simply Folded Belt. It has been shown that thrusts in form of reactivated normal faults can trigger out-of-sequence deformation within the sedimentary stratigraphy. Furthermore, deeply rooted strike-slip faults, such as the Kazerun faults between the Fars zone in the southeast and the Dezful embayment and the Izeh zone, are largely dispersing into the overlying stratigraphy, strongly influencing the tectonic evolution and mechanical behaviour. The aim of this study is to reveal the influence of basement thrusts and strike-slip faults on the structural evolution of the Simply Folded Belt depending on the occurrence of intercrustal weak horizons (Hormuz salt) and the rheology and thermal structure of the basement. Therefore, we present high-resolution 3D thermo-mechnical models with pre-existing, inversively reactivated normal faults or strike-slip faults within the basement. Numerical models are based on finite difference, marker-in-cell technique with (power-law) visco-plastic rheology accounting for brittle deformation. Preliminary results show that deep tectonic structures present in the basement may have crucial effects on the morphology and evolution of a fold-and-thrust belt above a major detachment horizon.

  7. A 3D alcoholic liver disease model on a chip.

    PubMed

    Lee, JaeSeo; Choi, BongHwan; No, Da Yoon; Lee, GeonHui; Lee, Seung-Ri; Oh, HyunJik; Lee, Sang-Hoon

    2016-03-14

    Alcohol is one of the main causes of liver diseases, and the development of alcoholic liver disease (ALD) treatment methods has been one of the hottest issues. For this purpose, development of in vitro models mimicking the in vivo physiology is one of the critical requirements, and they help to determine the disease mechanisms and to discover the treatment method. Herein, a three-dimensional (3D) ALD model was developed and its superior features in mimicking the in vivo condition were demonstrated. A spheroid-based microfluidic chip was employed for the development of the 3D in vitro model of ALD progression. We co-cultured rat primary hepatocytes and hepatic stellate cells (HSCs) in a fluidic chip to investigate the role of HSCs in the recovery of liver with ALD. An interstitial level of flow derived by an osmotic pump was applied to the chip to provide in vivo mimicking of fluid activity. Using this in vitro tool, we were able to observe structural changes and decreased hepatic functions with the increase in ethanol concentration. The recovery process of liver injured by alcohol was observed by providing fresh culture medium to the damaged 3D liver tissue for few days. A reversibly- and irreversibly-injured ALD model was established. The proposed model can not only be used for the research of alcoholic disease mechanism, but also has the potential for use in studies of hepatotoxicity and drug screening applications. PMID:26857817

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

    NASA Astrophysics Data System (ADS)

    Jaiswal, Neeru; Kishtawal, C. M.

    2016-05-01

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

  9. Progress Toward an Integration of Process-Structure-Property-Performance Models for "Three-Dimensional (3-D) Printing" of Titanium Alloys

    NASA Astrophysics Data System (ADS)

    Collins, P. C.; Haden, C. V.; Ghamarian, I.; Hayes, B. J.; Ales, T.; Penso, G.; Dixit, V.; Harlow, G.

    2014-07-01

    Electron beam direct manufacturing, synonymously known as electron beam additive manufacturing, along with other additive "3-D printing" manufacturing processes, are receiving widespread attention as a means of producing net-shape (or near-net-shape) components, owing to potential manufacturing benefits. Yet, materials scientists know that differences in manufacturing processes often significantly influence the microstructure of even widely accepted materials and, thus, impact the properties and performance of a material in service. It is important to accelerate the understanding of the processing-structure-property relationship of materials being produced via these novel approaches in a framework that considers the performance in a statistically rigorous way. This article describes the development of a process model, the assessment of key microstructural features to be incorporated into a microstructure simulation model, a novel approach to extract a constitutive equation to predict tensile properties in Ti-6Al-4V (Ti-64), and a probabilistic approach to measure the fidelity of the property model against real data. This integrated approach will provide designers a tool to vary process parameters and understand the influence on performance, enabling design and optimization for these highly visible manufacturing approaches.

  10. 3D Face Modeling Using the Multi-Deformable Method

    PubMed Central

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

    2012-01-01

    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. PMID:23201976