Science.gov

Sample records for 3d structure analysis

  1. Advancements in 3D Structural Analysis of Geothermal Systems

    SciTech Connect

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

    2013-06-23

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

  2. 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.

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

    1999-11-22

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

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

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.

    1989-01-01

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

  5. CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures.

    PubMed

    Vlahovicek, Kristian; Pintar, Alessandro; Parthasarathi, Laavanya; Carugo, Oliviero; Pongor, Sándor

    2005-07-01

    The WWW servers at http://www.icgeb.org/protein/ are dedicated to the analysis of protein 3D structures submitted by the users as the Protein Data Bank (PDB) files. CX computes an atomic protrusion index that makes it possible to highlight the protruding atoms within a protein 3D structure. DPX calculates a depth index for the buried atoms and makes it possible to analyze the distribution of buried residues. CX and DPX return PDB files containing the calculated indices that can then be visualized using standard programs, such as Swiss-PDBviewer and Rasmol. PRIDE compares 3D structures using a fast algorithm based on the distribution of inter-atomic distances. The options include pairwise as well as multiple comparisons, and fold recognition based on searching the CATH fold database. PMID:15980464

  6. New insights into high resolution DEM structural analysis with Coltop3D software

    NASA Astrophysics Data System (ADS)

    Metzger, R.; Jaboyedoff, M.; Oppikofer, T.

    2009-04-01

    Modern measurement devices such a terrestrial laser scanning (TLS) systems allow for collecting tremendous amount of (x,y,z) points (up to 20 millions) within a few minutes. However, data analysis still may be impaired because of software limitations, which are usually not designed to handle such huge data sets. To overcome this shortcoming, a software - Coltop3D - was written from scratch. Coltop3D aims at providing the geosciences community a powerful tool to visually handle seamlessly large point clouds and large regular grids DEM, at allowing for straightforward visual analysis of the data with different colour scheme, and at providing specific geologist and/or geoscientist treatment methods such as structural analysis. The main features of Coltop3D are as follow: 1) Ability to handle huge data sets (up to 150 millions points); 2) Coloring the surface with a color scheme linking computer graphics HSV wheel and Schmidt-Lambert stereonet projection; 3) Ability to select a subset of a point cloud with complex geometric shapes; 4) Ability to select a subset of a point cloud with dip and dip direction values; 5) Creating density stereonets with selected subset; 6) Easily import from or export point cloud data to third party software. Besides the technical and basic capabilities of Coltop3D, specific case studies such as structural analysis and rock fall analysis will be presented.

  7. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  8. 3D structure tensor analysis of light microscopy data for validating diffusion MRI.

    PubMed

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A; Kohama, Steven G; Jespersen, Sune Nørhøj; Kroenke, Christopher D

    2015-05-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image "stacks" acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations that

  9. Performance analysis of high quality parallel preconditioners applied to 3D finite element structural analysis

    SciTech Connect

    Kolotilina, L.; Nikishin, A.; Yeremin, A.

    1994-12-31

    The solution of large systems of linear equations is a crucial bottleneck when performing 3D finite element analysis of structures. Also, in many cases the reliability and robustness of iterative solution strategies, and their efficiency when exploiting hardware resources, fully determine the scope of industrial applications which can be solved on a particular computer platform. This is especially true for modern vector/parallel supercomputers with large vector length and for modern massively parallel supercomputers. Preconditioned iterative methods have been successfully applied to industrial class finite element analysis of structures. The construction and application of high quality preconditioners constitutes a high percentage of the total solution time. Parallel implementation of high quality preconditioners on such architectures is a formidable challenge. Two common types of existing preconditioners are the implicit preconditioners and the explicit preconditioners. The implicit preconditioners (e.g. incomplete factorizations of several types) are generally high quality but require solution of lower and upper triangular systems of equations per iteration which are difficult to parallelize without deteriorating the convergence rate. The explicit type of preconditionings (e.g. polynomial preconditioners or Jacobi-like preconditioners) require sparse matrix-vector multiplications and can be parallelized but their preconditioning qualities are less than desirable. The authors present results of numerical experiments with Factorized Sparse Approximate Inverses (FSAI) for symmetric positive definite linear systems. These are high quality preconditioners that possess a large resource of parallelism by construction without increasing the serial complexity.

  10. New Approach for 3D Local Structure Refinement Using Non-Muffin-Tin XANES Analysis

    SciTech Connect

    Smolentsev, Grigory; Soldatov, Alexander V.; Feiters, Martin C.

    2007-02-02

    A new technique of 3D local structure refinement using full-potential X-ray absorption near edge structure (XANES) analysis is proposed and demonstrated in application to metalloorganic complexes of Ni. It can be applied to determine local structure in those cases where the muffin-tin approximation used in most full multiple scattering schemes fails. The method is based on the fitting of experimental XANES data using multidimensional interpolation of spectra as a function of structural parameters, recently proposed by us, and ab-initio full potential calculations of XANES using finite difference method. The small number of required ab-initio calculations is the main advantage of the approach, which allows one to use computationally time-expensive non-muffin-tin finite-difference method. The possibility to extract information on bond angles in addition to bond-lengths accessible to standard EXAFS is demonstrated and it opens new perspectives of quantitative XANES analysis as a 3D local structure probe.

  11. Comparative 3D genome structure analysis of the fission and the budding yeast.

    PubMed

    Gong, Ke; Tjong, Harianto; Zhou, Xianghong Jasmine; Alber, Frank

    2015-01-01

    We studied the 3D structural organization of the fission yeast genome, which emerges from the tethering of heterochromatic regions in otherwise randomly configured chromosomes represented as flexible polymer chains in an nuclear environment. This model is sufficient to explain in a statistical manner many experimentally determined distinctive features of the fission yeast genome, including chromatin interaction patterns from Hi-C experiments and the co-locations of functionally related and co-expressed genes, such as genes expressed by Pol-III. Our findings demonstrate that some previously described structure-function correlations can be explained as a consequence of random chromatin collisions driven by a few geometric constraints (mainly due to centromere-SPB and telomere-NE tethering) combined with the specific gene locations in the chromosome sequence. We also performed a comparative analysis between the fission and budding yeast genome structures, for which we previously detected a similar organizing principle. However, due to the different chromosome sizes and numbers, substantial differences are observed in the 3D structural genome organization between the two species, most notably in the nuclear locations of orthologous genes, and the extent of nuclear territories for genes and chromosomes. However, despite those differences, remarkably, functional similarities are maintained, which is evident when comparing spatial clustering of functionally related genes in both yeasts. Functionally related genes show a similar spatial clustering behavior in both yeasts, even though their nuclear locations are largely different between the yeast species.

  12. Analysis of simple 2-D and 3-D metal structures subjected to fragment impact

    NASA Technical Reports Server (NTRS)

    Witmer, E. A.; Stagliano, T. R.; Spilker, R. L.; Rodal, J. J. A.

    1977-01-01

    Theoretical methods were developed for predicting the large-deflection elastic-plastic transient structural responses of metal containment or deflector (C/D) structures to cope with rotor burst fragment impact attack. For two-dimensional C/D structures both, finite element and finite difference analysis methods were employed to analyze structural response produced by either prescribed transient loads or fragment impact. For the latter category, two time-wise step-by-step analysis procedures were devised to predict the structural responses resulting from a succession of fragment impacts: the collision force method (CFM) which utilizes an approximate prediction of the force applied to the attacked structure during fragment impact, and the collision imparted velocity method (CIVM) in which the impact-induced velocity increment acquired by a region of the impacted structure near the impact point is computed. The merits and limitations of these approaches are discussed. For the analysis of 3-d responses of C/D structures, only the CIVM approach was investigated.

  13. 3D structure determination of protein using TEM single particle analysis.

    PubMed

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  14. Analysis of hybrid dielectric-plasmonic slot waveguide structures with 3D Fourier Modal Methods

    NASA Astrophysics Data System (ADS)

    Ctyroky, J.; Kwiecien, P.; Richter, I.

    2013-03-01

    Recently, plasmonic waveguides have been intensively studied as promising basic building blocks for the construction of extremely compact photonic devices with subwavelength characteristic dimensions. A number of different types of plasmonic waveguide structures have been recently proposed, theoretically analyzed, and their properties experimentally verified. The fundamental trade-off in the design of plasmonic waveguides for potential application in information technologies lies in the contradiction between their mode field confinement and propagation loss: the higher confinement, the higher loss, and vice versa. Various definitions of figures of merit of plasmonic waveguides have been also introduced for the characterization of their properties with a single quantity. In this contribution, we theoretically analyze one specific type of a plasmonic waveguide - the hybrid dielectric-loaded plasmonic waveguide, or - as we call it in this paper - the hybrid dielectric-plasmonic slot waveguide, which exhibits very strong field confinement combined with acceptable losses allowing their application in some integrated plasmonic devices. In contrast to the structures analyzed previously, our structure makes use of a single low-index dielectric only. We first define the effective area of this waveguide type, and using waveguide parameters close to the optimum we analyze several waveguide devices as directional couplers, multimode interference couplers (MMI), and the Mach-Zehnder interferometer based on the MMI couplers. For the full-vector 3D analysis of these structures, we use modelling tools developed in-house on the basis of the Fourier Modal Method (FMM). Our results thus serve to a dual purpose: they confirm that (i) these structures represent promising building blocks of plasmonic devices, and (ii) our FMM codes are capable of efficient 3D vector modelling of plasmonic waveguide devices.

  15. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

    NASA Astrophysics Data System (ADS)

    Mu, Jian; Yang, Lin; Kamocka, Malgorzata M.; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

    2015-03-01

    In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

  16. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

    PubMed Central

    Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A.; Larabell, Carolyn A.; Chen, Lin; Alber, Frank

    2016-01-01

    Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm the presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization. PMID:26951677

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

    NASA Astrophysics Data System (ADS)

    Bhavanam, Sharada

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

  18. Error analysis for creating 3D face templates based on cylindrical quad-tree structure

    NASA Astrophysics Data System (ADS)

    Gutfeter, Weronika

    2015-09-01

    Development of new biometric algorithms is parallel to advances in technology of sensing devices. Some of the limitations of the current face recognition systems may be eliminated by integrating 3D sensors into these systems. Depth sensing devices can capture a spatial structure of the face in addition to the texture and color. This kind of data is yet usually very voluminous and requires large amount of computer resources for being processed (face scans obtained with typical depth cameras contain more than 150 000 points per face). That is why defining efficient data structures for processing spatial images is crucial for further development of 3D face recognition methods. The concept described in this work fulfills the aforementioned demands. Modification of the quad-tree structure was chosen because it can be easily transformed into less dimensional data structures and maintains spatial relations between data points. We are able to interpret data stored in the tree as a pyramid of features which allow us to analyze face images using coarse-to-fine strategy, often exploited in biometric recognition systems.

  19. Development of computer program NAS3D using Vector processing for geometric nonlinear analysis of structures

    NASA Technical Reports Server (NTRS)

    Mangalgiri, P. D.; Prabhakaran, R.

    1986-01-01

    An algorithm for vectorized computation of stiffness matrices of an 8 noded isoparametric hexahedron element for geometric nonlinear analysis was developed. This was used in conjunction with the earlier 2-D program GAMNAS to develop the new program NAS3D for geometric nonlinear analysis. A conventional, modified Newton-Raphson process is used for the nonlinear analysis. New schemes for the computation of stiffness and strain energy release rates is presented. The organization the program is explained and some results on four sample problems are given. The study of CPU times showed that savings by a factor of 11 to 13 were achieved when vectorized computation was used for the stiffness instead of the conventional scalar one. Finally, the scheme of inputting data is explained.

  20. Error analysis and system implementation for structured light stereo vision 3D geometric detection in large scale condition

    NASA Astrophysics Data System (ADS)

    Qi, Li; Zhang, Xuping; Wang, Jiaqi; Zhang, Yixin; Wang, Shun; Zhu, Fan

    2012-11-01

    Stereo vision based 3D metrology technique is an effective approach for relatively large scale object's 3D geometric detection. In this paper, we present a specified image capture system, which implements LVDS interface embedded CMOS sensor and CAN bus to ensure synchronous trigger and exposure. We made an error analysis for structured light vision measurement in large scale condition, based on which we built and tested the system prototype both indoor and outfield. The result shows that the system is very suitable for large scale metrology applications.

  1. 3D-FE analysis of functionally graded structured dental posts.

    PubMed

    Abu Kasim, Noor H; Madfa, Ahmed A; Hamdi, Mohd; Rahbari, Ghahnavyeh R

    2011-01-01

    This study aimed to compare the biomechanical behaviour of functionally graded structured posts (FGSPs) and homogenous-type posts in simulated models of a maxillary central incisor. Two models of FGSPs consisting of a multilayer xTi-yHA composite design, where zirconia and alumina was added as the first layer for models A and B respectively were compared to homogenous zirconia post (model C) and a titanium post (model D). The amount of Ti and HA in the FGSP models was varied in gradations. 3D-FEA was performed on all models and stress distributions were investigated along the dental post. In addition, interface stresses between the posts and their surrounding structures were investigated under vertical, oblique, and horizontal loadings. Strain distribution along the post-dentine interface was also investigated. The results showed that FGSPs models, A and B demonstrated better stress distribution than models C and D, indicating that dental posts with multilayered structure dissipate localized and interfacial stress and strain more efficiently than homogenous-type posts. PMID:22123011

  2. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    SciTech Connect

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A.; Zadoks, R.I.

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  3. Constructing topologically connected surfaces for the comprehensive analysis of 3-D medical structures

    NASA Astrophysics Data System (ADS)

    Kalvin, Alan D.; Cutting, Court B.; Haddad, Betsy; Noz, Marilyn E.

    1991-06-01

    Three-dimensional (3D) medical imaging deals with the visualization, manipulation, and measuring of objects in 3D medical images. So far, research efforts have concentrated primarily on visualization, using well-developed methods from computer graphics. Very little has been achieved in developing techniques for manipulating medical objects, or for extracting quantitative measurements from them beyond volume calculation (by counting voxels), and computing distances and angles between manually located surface points. A major reason for the slow pace in the development of manipulation and quantification methods lies with the limitations of current algorithms for constructing surfaces from 3D solid objects. We show that current surface construction algorithms either (a) do not construct valid surface descriptions of solid objects or (b) produce surface representations that are not particularly suitable for anything other than visualization. We present ALLIGATOR, a new surface construction algorithm that produces valid, topologically connected surface representations of solid objects. We have developed a modeling system based on the surface representations created by ALLIGATOR that is suitable for developing algorithms to visualize, manipulate, and quantify 3D medical objects. Using this modeling system we have developed a method for efficiently computing principle curvatures and directions on surfaces. These measurements form the basis for a new metric system being developed for morphometrics. The modeling system is also being used in the development of systems for quantitative pre-surgical planning and surgical augmentation.

  4. Construction of topological structure of 3D coronary vessels for analysis of catheter navigation in interventional cardiology simulation

    NASA Astrophysics Data System (ADS)

    Wang, Yaoping; Chui, Cheekong K.; Cai, Yiyu; Mak, KoonHou

    1998-06-01

    This study presents an approach to build a 3D vascular system of coronary for the development of a virtual cardiology simulator. The 3D model of the coronary arterial tree is reconstructed from the geometric information segmented from the Visible Human data set for physical analysis of catheterization. The process of segmentation is guided by a 3D topologic hierarchy structure of coronary vessels which is obtained from a mechanical model by using Coordinate Measuring Machine (CMM) probing. This mechanical professional model includes all major coronary arterials ranging from right coronary artery to atrioventricular branch and from left main trunk to left anterior descending branch. All those branches are considered as the main operating sites for cardiology catheterization. Along with the primary arterial vasculature and accompanying secondary and tertiary networks obtained from a previous work, a more complete vascular structure can then be built for the simulation of catheterization. A novel method has been developed for real time Finite Element Analysis of catheter navigation based on this featured vasculature of vessels.

  5. A fast technique applied to the analysis of Resistive Wall Modes with 3D conducting structures

    SciTech Connect

    Rubinacci, Guglielmo Liu, Yueqiang

    2009-03-20

    This paper illustrates the development of a 'fast' technique for the analysis of Resistive Wall Modes (RWMs) in fusion devices with three-dimensional conducting structures, by means of the recently developed CarMa code. Thanks to its peculiar features, the computational cost scales almost linearly with the number of discrete unknowns. Some large scale problems are solved in configurations of interest for the International Thermonuclear Experimental Reactor (ITER)

  6. Classification of mathematics deficiency using shape and scale analysis of 3D brain structures

    NASA Astrophysics Data System (ADS)

    Kurtek, Sebastian; Klassen, Eric; Gore, John C.; Ding, Zhaohua; Srivastava, Anuj

    2011-03-01

    We investigate the use of a recent technique for shape analysis of brain substructures in identifying learning disabilities in third-grade children. This Riemannian technique provides a quantification of differences in shapes of parameterized surfaces, using a distance that is invariant to rigid motions and re-parameterizations. Additionally, it provides an optimal registration across surfaces for improved matching and comparisons. We utilize an efficient gradient based method to obtain the optimal re-parameterizations of surfaces. In this study we consider 20 different substructures in the human brain and correlate the differences in their shapes with abnormalities manifested in deficiency of mathematical skills in 106 subjects. The selection of these structures is motivated in part by the past links between their shapes and cognitive skills, albeit in broader contexts. We have studied the use of both individual substructures and multiple structures jointly for disease classification. Using a leave-one-out nearest neighbor classifier, we obtained a 62.3% classification rate based on the shape of the left hippocampus. The use of multiple structures resulted in an improved classification rate of 71.4%.

  7. 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.

  8. Structural evolution of the VMS-hosting Kristineberg area, Sweden - constraints from structural analysis and 3-D-modelling

    NASA Astrophysics Data System (ADS)

    Skyttä, P.; Bauer, T.; Hermansson, T.; Dehghannejad, M.; Juhlin, C.; García, M.; Hübert, J.; Weihed, P.

    2012-10-01

    Structural mapping and 3-D-modelling with constraints from magnetotelluric (MT) and reflection seismic investigations have been used to provide a geological synthesis of the geometrically complex Kristineberg area in the western part of the Palaeoproterozoic Skellefte district. The results indicate that, like the south-eastern parts of the Skellefte district, the area was subjected to SSE-NNW transpressional deformation at around 1.87 Ga. The contrasting structural geometries between the Kristineberg and the central Skellefte district areas may be attributed to the termination and splaying of a major ESE-WNW-striking high-strain zone into several branches in the northern part of the Kristineberg area. The transpressional structural signature was preferentially developed within the southern of the two antiformal structures of the area, "the Southern antiform", which exposes the deepest cut through the crust and hosts all the economic volcanogenic massive sulphides (VMS) deposits of the area. Partitioning of the SSE-NNW transpression into N-S and E-W components led to formation of a characteristic "flat-steep-flat" geometry defining a highly non-cylindrical hinge of for the Southern antiform. Recognition of the transpressional structural signatures including the "flat-steep-flat" geometry and the distinct pattern of sub-horizontal E-W trending to moderately SW-plunging mineral lineations in the deeper crustal parts of the Kristineberg area is of significance for VMS exploration in both near mine and regional scales. The 3-D-model illustrating the outcomes of this study is available as a 3-D-PDF document through the publication website.

  9. Automated Assignment of MS/MS Cleavable Cross-Links in Protein 3D-Structure Analysis

    NASA Astrophysics Data System (ADS)

    Götze, Michael; Pettelkau, Jens; Fritzsche, Romy; Ihling, Christian H.; Schäfer, Mathias; Sinz, Andrea

    2015-01-01

    CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .

  10. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

    PubMed

    Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S; Carazo, Jose Maria

    2016-02-23

    Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application-3DIANA-specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es.

  11. 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/.

  12. 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

  13. A Mean Field Analysis of the Exchange Coupling (J) For 2- and 3-D Structured Tetracyanoethylenide (TCNE -)-based Magnets

    SciTech Connect

    McConnell, Amber C.; Fishman, Randy Scott; Miller, Joel S.

    2012-01-01

    Mean field expressions based on the simple Heisenberg model were derived to correlate the inter- and intralayer exchange coupling to the critical temperatures, Tc, for several TCNE (tetracyanoethylene) based magnets with extended 2- and 3-D structure types. These expressions were used to estimate the exchange coupling, J, for 2-D ferrimagnetic [MII(TCNE)(NCMe)2]+ (M = Mn, Fe), 3-D antiferromagnetic MnII(TCNE)[C4(CN)8]1/2, and 3-D ferrimagnetic MnII(TCNE)3/2(I3)1/2. The sign and magnitude of the exchange coupling are in accord with previously reported magnetic data.

  14. Self assembled structures for 3D integration

    NASA Astrophysics Data System (ADS)

    Rao, Madhav

    Three dimensional (3D) micro-scale structures attached to a silicon substrate have various applications in microelectronics. However, formation of 3D structures using conventional micro-fabrication techniques are not efficient and require precise control of processing parameters. Self assembly is a method for creating 3D structures that takes advantage of surface area minimization phenomena. Solder based self assembly (SBSA), the subject of this dissertation, uses solder as a facilitator in the formation of 3D structures from 2D patterns. Etching a sacrificial layer underneath a portion of the 2D pattern allows the solder reflow step to pull those areas out of the substrate plane resulting in a folded 3D structure. Initial studies using the SBSA method demonstrated low yields in the formation of five different polyhedra. The failures in folding were primarily attributed to nonuniform solder deposition on the underlying metal pads. The dip soldering method was analyzed and subsequently refined. A modified dip soldering process provided improved yield among the polyhedra. Solder bridging referred as joining of solder deposited on different metal patterns in an entity influenced the folding mechanism. In general, design parameters such as small gap-spacings and thick metal pads were found to favor solder bridging for all patterns studied. Two types of soldering: face and edge soldering were analyzed. Face soldering refers to the application of solder on the entire metal face. Edge soldering indicates application of solder only on the edges of the metal face. Mechanical grinding showed that face soldered SBSA structures were void free and robust in nature. In addition, the face soldered 3D structures provide a consistent heat resistant solder standoff height that serve as attachments in the integration of dissimilar electronic technologies. Face soldered 3D structures were developed on the underlying conducting channel to determine the thermo-electric reliability of

  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. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    NASA Astrophysics Data System (ADS)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  18. 3D Finite Element Analysis of Some Structural Modified PC Sleeper with the Vibration Characteristics between Sleeper and Ballast

    NASA Astrophysics Data System (ADS)

    Sakai, Hirotaka; Urakawa, Fumihiro; Aikawa, Akira; Namura, Akira

    The vibration of concrete sleepers is an important factor engendering track deterioration. In this paper, we created a three-dimensional finite element model to reproduce a prestressed concrete (PC) sleeper in detail, expressing influence of ballast layers with a 3D spring series and dampers to reproduce their vibration and dynamic characteristics. Determination of these parameters bases on the experimental modal analysis using an impact excitation technique for PC sleepers by adjusting the accelerance between the analytical results and experimental results. Furthermore, we compared the difference of these characteristics between normal sleepers and those with some structural modifications. Analytical results clarified that such means as sleeper width extension and increased sleeper thickness will influence the reduction of ballasted track vibration as improvements of PC sleepers.

  19. 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

  20. Analysis of time-structure of BSRs using 3D seismic data in the Eastern Nankai Trough, Japan

    NASA Astrophysics Data System (ADS)

    Nagakubo, S.; Inamori, T.; Kobayashi, T.; Fujii, T.

    2005-12-01

    According to the result of METI Exploratory Wells "Tokai-Oki to Kumano-nada" conducted in FY2003 in Japan, it is suggested that methane hydrate bearing layers in the Eastern Nanakai Trough distribute heterogeneously above BSRs (Bottom Simulating Reflectors). To understand the heterogeneity of distribution of methane hydrate bearing layers and explore concentrated hydrate bearing layers, we conducted a detailed analysis of time-structure map of BSR using 3D seismic survey data acquired in the Eastern Nankai Trough. Since P-wave velocity of hydrate bearing layers are high, it was expected that two-way-time from sea bottom to BSR is short above concentrated hydrate bearing layers compared to hydrate bearing zones. Although significant anomalies are recognized on time-structure map, it seems that anomalies are corresponding to heterogeneous thermal-structure in preference to distribution of hydrate bearing layers around surveyed area. It should be considered that these thermal anomalies are depending on fluid migration with hydrocarbons through faults, unconformities and permeable sand layers from deeper formations. Since occurrences of methane hydrates are strongly restricted by temperature and pressure, analysis of time-structure of BSR acquired by seismic data could be helpful to understand the accumulation mechanism of methane hydrates in sediments.

  1. 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

  2. Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System

    PubMed Central

    Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

    2016-01-01

    While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments. PMID:27598174

  3. Analysis and Compensation for Lateral Chromatic Aberration in a Color Coding Structured Light 3D Measurement System.

    PubMed

    Huang, Junhui; Xue, Qi; Wang, Zhao; Gao, Jianmin

    2016-01-01

    While color-coding methods have improved the measuring efficiency of a structured light three-dimensional (3D) measurement system, they decreased the measuring accuracy significantly due to lateral chromatic aberration (LCA). In this study, the LCA in a structured light measurement system is analyzed, and a method is proposed to compensate the error caused by the LCA. Firstly, based on the projective transformation, a 3D error map of LCA is constructed in the projector images by using a flat board and comparing the image coordinates of red, green and blue circles with the coordinates of white circles at preselected sample points within the measurement volume. The 3D map consists of the errors, which are the equivalent errors caused by LCA of the camera and projector. Then in measurements, error values of LCA are calculated and compensated to correct the projector image coordinates through the 3D error map and a tri-linear interpolation method. Eventually, 3D coordinates with higher accuracy are re-calculated according to the compensated image coordinates. The effectiveness of the proposed method is verified in the following experiments. PMID:27598174

  4. 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

  5. User's manual for FRAC3D: Supplement to report on stress analysis for structures with surface cracks

    NASA Technical Reports Server (NTRS)

    Bell, J. C.; Hopper, A. T.; Hayes, P. A.

    1978-01-01

    The FRAC3D computer program, designed for use in analyzing stresses in structures (including plates, bars, or blocks) which may contain part-circular surface cracks or embedded circular cracks is described. Instructions are provided for preparing input, including that for the supporting programs LATTICE and MATSOL as well as for FRAC3D. The course of a substantial illustrative calculation is shown with both input and output. The formulas underlying the calculations are summarized and related to the subroutines in which they are used. Many issues of strategy in using this program for analysing stresses around surface cracks are elucidated.

  6. A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification

    PubMed Central

    Dong, Xiaoqing; Fang, Yiliang; Wang, Kejing; Zhu, Lijuan; Wang, Ke; Huang, Tao

    2016-01-01

    With the development of new technologies in transcriptome and epigenetics, RNAs have been identified to play more and more important roles in life processes. Consequently, various methods have been proposed to assess the biological functions of RNAs and thus classify them functionally, among which comparative study of RNA structures is perhaps the most important one. To measure the structural similarity of RNAs and classify them, we propose a novel three dimensional (3D) graphical representation of RNA secondary structure, in which an RNA secondary structure is first transformed into a characteristic sequence based on chemical property of nucleic acids; a dynamic 3D graph is then constructed for the characteristic sequence; and lastly a numerical characterization of the 3D graph is used to represent the RNA secondary structure. We tested our algorithm on three datasets: (1) Dataset I consisting of nine RNA secondary structures of viruses, (2) Dataset II consisting of complex RNA secondary structures including pseudo-knots, and (3) Dataset III consisting of 18 non-coding RNA families. We also compare our method with other nine existing methods using Dataset II and III. The results demonstrate that our method is better than other methods in similarity measurement and classification of RNA secondary structures. PMID:27213271

  7. Structural design, layout analysis and routing strategy for constructing IC standard cells using emerging 3D vertical MOSFETs

    NASA Astrophysics Data System (ADS)

    Liu, Hongyi; Hong, Chuyang; Han, Ting; Zhou, Jun; Chen, Yijian

    2016-03-01

    As optical lithography and conventional transistor structure are approaching their physical limits, 3D vertical gate-all-around (GAA) nanowire MOSFETs and double-surrounding-gate (DSG) MOSFETs are two promising device candidates for post-FinFET logic scaling owing to their superior gate control and scaling potential. However, source, drain and gate of a vertical nanowire MOSFET and DSG MOSFETs are located in different physical layers. Consequently, structural design of IC devices/circuits, layout arrangement for high-density vertical nanowires/interconnects, and routing strategy are non-trivial challenges. In this paper, we shall discuss these critical issues for constructing standard cells using 3D vertical GAA nanowire MOSFETs and DSG MOSFETs. We redesigned the standard cells in Nangate Open Cell Library for 5nm node using vertical GAA nanowire MOSFETs and DSG MOSFETs. Experimental results verify the functionality of the proposed standard cell layout design approach.

  8. Seismic attribute analysis for 3-D structural interpretation of the offshore South Marsh Island, Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Horozal, Senay; Lee, Gwang Hoon; Cukur, Deniz; Pigott, John D.

    2013-04-01

    Structural and seismic attribute analyses of 3-D seismic reflection data from southwest offshore South Marsh Island, Louisiana, Gulf of Mexico, reveal complex structures affected by salt tectonics triggered by interaction between salt, faults and rapid deltaic sedimentation on the shallow continental shelf. Salt exercises the main control on the sedimentary processes in the study area to move, to divert sediment, to create instability, and to block sediment transport pathways. The depths of salt range about 4,300 m (14,000 ft) to 6,500 m (21,600 ft). Salt is very deep and forms a thin sheet in the southwestern part of the area, whereas it rises to shallow depths, forming a dome in the central part. Salt is seen at relatively shallow stratigraphic levels in the northwest and south where it forms thin salt rollers. The margins of Miocene strata are deformed by salt movement and faulting in the study area. The study area is riddled by numerous normal faults which are mostly E-trending and some N- and NW-trending with southward gradual increase in growth factors. Eight main normal faults were interpreted from seismic data which are mostly E-trending S-dipping, and are accompanied by smaller secondary faults. Three of E-trending down-to-the-basin growth faults cut across the study area separating the area into four blocks. These faults form a stair-stepping structure in the south direction. Two conjugate-crossing normal faults are located over the central salt dome which may indicate active salt doming. Seismic attribute analysis was applied as output of seismic volumes, and horizon and time-slice maps in order to identify the structure of study area. These attribute volumes together with time- and horizon-slices gave amplitude anomalies at discontinuities (faults) and lithological changes (sand to shale, salt). Faults interpreted and mapped from seismic profiles and those identified by seismic attribute slices are compatible, therefore, seismic attribute analysis can

  9. 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.

  10. Motif3D: Relating protein sequence motifs to 3D structure.

    PubMed

    Gaulton, Anna; Attwood, Teresa K

    2003-07-01

    Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

  11. Multifractal analysis of white matter structural changes on 3D magnetic resonance imaging between normal aging and early Alzheimer’s disease

    NASA Astrophysics Data System (ADS)

    Ni, Huang-Jing; Zhou, Lu-Ping; Zeng, Peng; Huang, Xiao-Lin; Liu, Hong-Xing; Ning, Xin-Bao

    2015-07-01

    Applications of multifractal analysis to white matter structure changes on magnetic resonance imaging (MRI) have recently received increasing attentions. Although some progresses have been made, there is no evident study on applying multifractal analysis to evaluate the white matter structural changes on MRI for Alzheimer’s disease (AD) research. In this paper, to explore multifractal analysis of white matter structural changes on 3D MRI volumes between normal aging and early AD, we not only extend the traditional box-counting multifractal analysis (BCMA) into the 3D case, but also propose a modified integer ratio based BCMA (IRBCMA) algorithm to compensate for the rigid division rule in BCMA. We verify multifractal characteristics in 3D white matter MRI volumes. In addition to the previously well studied multifractal feature, Δα, we also demonstrated Δf as an alternative and effective multifractal feature to distinguish NC from AD subjects. Both Δα and Δf are found to have strong positive correlation with the clinical MMSE scores with statistical significance. Moreover, the proposed IRBCMA can be an alternative and more accurate algorithm for 3D volume analysis. Our findings highlight the potential usefulness of multifractal analysis, which may contribute to clarify some aspects of the etiology of AD through detection of structural changes in white matter. Project supported by the National Natural Science Foundation of China (Grant No. 61271079), the Vice Chancellor Research Grant in University of Wollongong, and the Priority Academic Program Development of Jiangsu Higher Education Institutions, China.

  12. Crustal density structure in northwestern South America derived from analysis and 3-D modeling of gravity and seismicity data

    NASA Astrophysics Data System (ADS)

    Sanchez-Rojas, J.; Palma, M.

    2014-11-01

    This paper presents a three-dimensional (3-D) interpretation of new gravity and seismicity datasets for northern South America. A 3-D forward density model was constructed on the basis of deep wide-angle seismic refraction sections, Moho depth from receiver functions, and surface geology. Density values were estimated from published borehole data for sediments by using empirical velocity-density functions and considering mineralogical-chemical composition variations under typical pressure-temperature conditions for upper and lower crustal rocks. The modeled 3-D density structure was kept as simple as possible. The continental and oceanic plates were formed by two sedimentary bodies, one crustal body, and one mantle lithosphere body overlying a sub-lithospheric mantle. The Caribbean plate was modeled with an atypical crustal thickness of ~ 18 km (including sediments). The geometry of the Caribbean plate was modeled using a combination of gravity modeling and analyses of the seismicity and focal-mechanism solutions. Intermediate seismicity and the orientation of the T-axes appeared aligned along the predicted position of the slab. As a result, the estimated slab dip angle under Maracaibo and the Mérida Andes was ~ 15° and increases up to ~ 20° after 100 km depth. The model shows two orientations in the slab strike: ~ N150°E ± 5 in western Colombia and southward underneath the Maracaibo block. The modeling results suggest that the northern South American upper and lower crusts are relatively light and the density of the Caribbean crust is typical for an oceanic crust.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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…

  19. 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

  20. 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

  1. 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

  2. Negative refraction and focusing analysis in a left-handed material slab and realization with a 3D photonic crystal structure

    NASA Astrophysics Data System (ADS)

    Ahmadlou, Majid; Kamarei, Mahmoud; Sheikhi, Mohammad Hossein

    2006-02-01

    The increasing interest in metamaterials and structures with negative refraction index requires a formulation capable of a full analysis of wave propagation in such materials and structures. Since two-dimensional (2D) problems have been largely explored in the literature, the natural step is a three-dimensional (3D) formulation of these structures. In this paper, (3D) formulation and simulation of a left-handed metamaterial slab using the finite-difference time domain (FDTD) method in conjunction with perfectly matched layers (PMLs) is presented, and also a (3D) photonic crystal (PC) based structure is presented as a candidate for replacing the left-handed medium slab to realize the negative index of refraction on natural dielectric substrates. The results of these simulations are compared with each other, and the resulting outputs of the developed model are in good agreement. The results demonstrate numerically the focusing of the field emitted from an omnidirectional line source placed in front of the slab and crystal. Both the source and the focus pattern are away from the slab interfaces at two sides of the slab to have a real, negative perfect image. The dimensions of the simulation domain are set to have both source and image in the resulted plots. The focus pattern shows the ability of a photonic crystal structure in making a true flat lens.

  3. Design of 3d Topological Data Structure for 3d Cadastre Objects

    NASA Astrophysics Data System (ADS)

    Zulkifli, N. A.; Rahman, A. Abdul; Hassan, M. I.

    2016-09-01

    This paper describes the design of 3D modelling and topological data structure for cadastre objects based on Land Administration Domain Model (LADM) specifications. Tetrahedral Network (TEN) is selected as a 3D topological data structure for this project. Data modelling is based on the LADM standard and it is used five classes (i.e. point, boundary face string, boundary face, tetrahedron and spatial unit). This research aims to enhance the current cadastral system by incorporating 3D topology model based on LADM standard.

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

    PubMed

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

    2015-07-15

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

  5. 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

  6. Modeling and Analysis of Granite Matrix Pore Structure and Hydraulic Characteristics in 2D and 3D Networks

    NASA Astrophysics Data System (ADS)

    Gvozdik, L.; Polak, M.; Zaruba, J.; Vanecek, M.

    2010-12-01

    A geological environment labeled as a Granite massif represents in terms of groundwater flow and transport a distinct hydrogeological environment from that of sedimentary basins, the characterisation of which is generally more complex and uncertain. Massifs are composed of hard crystalline rocks with the very low effective porosity. Due to their rheological properties such rocks are predisposed to brittle deformation resulting from changes in stress conditions. Our specific research project (Research on the influence of intergrangular porosity on deep geological disposal: geological formations, methodology and the development of measurement apparatus) is focussed on the problem of permeable zones within apparently undisturbed granitic rock matrix. The project including the both laboratory and in-situ tracer tests study migration along and through mineral grains in fresh and altered granite. The objective of the project is to assess whether intergranular porosity is a general characteristic of the granitic rock matrix or subject to significant evolution resulting from geochemical and/or hydrogeochemical processes, geotechnical and/or mechanical processes. Moreover, the research is focussed on evaluating methods quantifying intergranular porosity by both physical testing and mathematical modelling using verified standard hydrological software tools. Groundwater flow in microfractures and intergranular pores in granite rock matrix were simulated in three standard hydrogeological modeling programs with completely different conceptual approaches: MODFLOW (Equivalent Continuum concept), FEFLOW (Discrete Fracture and Equivalent Continuum concepts) and NAPSAC (Discrete Fracture Network concept). Specialized random fracture generators were used for creation of several 2D and 3D models in each of the chosen program. Percolation characteristics of these models were tested and analyzed. Several scenarios of laboratory tests of the rock samples permeability made in triaxial

  7. 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

  8. Imaging and 3D morphological analysis of collagen fibrils.

    PubMed

    Altendorf, H; Decencière, E; Jeulin, D; De sa Peixoto, P; Deniset-Besseau, A; Angelini, E; Mosser, G; Schanne-Klein, M-C

    2012-08-01

    The recent booming of multiphoton imaging of collagen fibrils by means of second harmonic generation microscopy generates the need for the development and automation of quantitative methods for image analysis. Standard approaches sequentially analyse two-dimensional (2D) slices to gain knowledge on the spatial arrangement and dimension of the fibrils, whereas the reconstructed three-dimensional (3D) image yields better information about these characteristics. In this work, a 3D analysis method is proposed for second harmonic generation images of collagen fibrils, based on a recently developed 3D fibre quantification method. This analysis uses operators from mathematical morphology. The fibril structure is scanned with a directional distance transform. Inertia moments of the directional distances yield the main fibre orientation, corresponding to the main inertia axis. The collaboration of directional distances and fibre orientation delivers a geometrical estimate of the fibre radius. The results include local maps as well as global distribution of orientation and radius of the fibrils over the 3D image. They also bring a segmentation of the image into foreground and background, as well as a classification of the foreground pixels into the preferred orientations. This accurate determination of the spatial arrangement of the fibrils within a 3D data set will be most relevant in biomedical applications. It brings the possibility to monitor remodelling of collagen tissues upon a variety of injuries and to guide tissues engineering because biomimetic 3D organizations and density are requested for better integration of implants.

  9. 3D-FEM analysis of SPP excitation through nanoholes in asymmetric metal-insulator-metal structure at tip of circular truncated conical fiber

    NASA Astrophysics Data System (ADS)

    Oshikane, Y.; Murai, K.; Nakano, M.

    2014-09-01

    3D-electromagnetic (EM) analysis of surface plasmon polaritons (SPPs) excited by a single-mode (SM) propagation of visible lightwave in an optical fiber has been studied with a 3D-FEM package based on a finite element method. End of the fiber is formed to be a circular cone by wet etching process, and is FIBed to make a circular truncated conical shape with a flat circular surface a few micrometers in diameter. The flat end is covered with three layers of asymmetric metalinsulator- metal structure, thin metallic layer (M1), thick insulator layer (I), and thick metallic layer (M2), respectively. The outermost M2 layer has FIBed nanoholes to convert light waves at the extremity of the fiber into SPPs efficiently, and a bright tiny point light source will be generated on the surface of the M2 layer. In this study, the 3D-FEM models consists of both the MIM structure and the shrinking optical fiber tip coated with a metallic thin film has been designed and analyzed numerically. By applying perfect electric conductor and perfect magnetic conductor to planes containing the axis of rotation, the FEM model has a quarter of the circular truncated conical shape. The FEM analysis is formed in two steps. At the first step, a FEM mode analysis is performed to obtain a solution corresponding to the SM propagation in the fiber. The second level of action is the FEM analysis of EM field in the whole of model to find a stationary solution with the solution of mode analysis. Characteristic of wavelength-dependent excitation, propagation, and focusing of the SPPs will be presented with several experimental results of trial products of the fiber tip.

  10. The effect of spatial micro-CT image resolution and surface complexity on the morphological 3D analysis of open porous structures

    SciTech Connect

    Pyka, Grzegorz; Kerckhofs, Greet

    2014-01-15

    In material science microfocus X-ray computed tomography (micro-CT) is one of the most popular non-destructive techniques to visualise and quantify the internal structure of materials in 3D. Despite constant system improvements, state-of-the-art micro-CT images can still hold several artefacts typical for X-ray CT imaging that hinder further image-based processing, structural and quantitative analysis. For example spatial resolution is crucial for an appropriate characterisation as the voxel size essentially influences the partial volume effect. However, defining the adequate image resolution is not a trivial aspect and understanding the correlation between scan parameters like voxel size and the structural properties is crucial for comprehensive material characterisation using micro-CT. Therefore, the objective of this study was to evaluate the influence of the spatial image resolution on the micro-CT based morphological analysis of three-dimensional (3D) open porous structures with a high surface complexity. In particular the correlation between the local surface properties and the accuracy of the micro-CT-based macro-morphology of 3D open porous Ti6Al4V structures produced by selective laser melting (SLM) was targeted and revealed for rough surfaces a strong dependence of the resulting structure characteristics on the scan resolution. Reducing the surface complexity by chemical etching decreased the sensitivity of the overall morphological analysis to the spatial image resolution and increased the detection limit. This study showed that scan settings and image processing parameters need to be customized to the material properties, morphological parameters under investigation and the desired final characteristics (in relation to the intended functional use). Customization of the scan resolution can increase the reliability of the micro-CT based analysis and at the same time reduce its operating costs. - Highlights: • We examine influence of the image resolution

  11. Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis.

    PubMed

    Li, Jiazhong; Li, Shuyan; Bai, Chongliang; Liu, Huanxiang; Gramatica, Paola

    2013-07-01

    Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl-4(1H)-quinolone analogs, derived from the famous compound endochin, were reported as promising candidates for orally efficacious antimalarials. In this study, to analyze the structure-activity relationships (SAR) of these quinolones and investigate the structural requirements for antimalarial activity, the 2D multiple linear regressions (MLR) method and 3D comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods are employed to evolve different QSAR models. All these models give satisfactory results with highly accurate fitting and strong external predictive abilities for chemicals not used in model development. Furthermore, the contour maps from 3D models can provide an intuitive understanding of the key structure features responsible for the antimalarial activities. In conclusion, we summarize the detailed position-specific structural requirements of these derivatives accordingly. All these results are helpful for the rational design of new compounds with higher antimalarial bioactivities.

  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. SAMA: A Method for 3D Morphological Analysis.

    PubMed

    Paulose, Tessie; Montévil, Maël; Speroni, Lucia; Cerruti, Florent; Sonnenschein, Carlos; Soto, Ana M

    2016-01-01

    Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama. PMID:27035711

  14. SAMA: A Method for 3D Morphological Analysis

    PubMed Central

    Cerruti, Florent; Sonnenschein, Carlos; Soto, Ana M.

    2016-01-01

    Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama. PMID:27035711

  15. 3-D models and structural analysis of rock avalanches: the study of the deformation process to better understand the propagation mechanism

    NASA Astrophysics Data System (ADS)

    Longchamp, Céline; Abellan, Antonio; Jaboyedoff, Michel; Manzella, Irene

    2016-09-01

    Rock avalanches are extremely destructive and uncontrollable events that involve a great volume of material (> 106 m3) and several complex processes, and they are difficult to witness. For this reason the study of these phenomena using analog modeling and the accurate analysis of deposit structures and features of laboratory data and historic events become of great importance in the understanding of their behavior.The main objective of this research is to analyze rock avalanche dynamics and deformation process by means of a detailed structural analysis of the deposits coming from data of 3-D measurements of mass movements of different magnitudes, from decimeter level scale laboratory experiments to well-studied rock avalanches of several square kilometers' magnitude.Laboratory experiments were performed on a tilting plane on which a certain amount of a well-defined granular material is released, propagates and finally stops on a horizontal surface. The 3-D geometrical model of the deposit is then obtained using either a scan made with a 3-D digitizer (Konica Minolta VIVID 9i) or a photogrammetric method called structure from motion (SfM), which requires taking several pictures from different point of view of the object to be modeled.In order to emphasize and better detect the fault structures present in the deposits, we applied a median filter with different moving window sizes (from 3 × 3 to 9 × 9 nearest neighbors) to the 3-D datasets and a gradient operator along the direction of propagation.The application of these filters on the datasets results in (1) a precise mapping of the longitudinal and transversal displacement features observed at the surface of the deposits and (2) a more accurate interpretation of the relative movements along the deposit (i.e., normal, strike-slip, inverse faults) by using cross sections. Results show how the use of filtering techniques reveals disguised features in the original point cloud and that similar displacement patterns

  16. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    PubMed

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  17. 3D Network Analysis for Indoor Space Applications

    NASA Astrophysics Data System (ADS)

    Tsiliakou, E.; Dimopoulou, E.

    2016-10-01

    Indoor space differs from outdoor environments, since it is characterized by a higher level of structural complexity, geometry, as well as topological relations. Indoor space can be considered as the most important component in a building's conceptual modelling, on which applications such as indoor navigation, routing or analysis are performed. Therefore, the conceptual meaning of sub spaces or the activities taking place in physical building boundaries (e.g. walls), require the comprehension of the building's indoor hierarchical structure. The scope of this paper is to perform 3D network analysis in a building's interior and is structured as follows: In Section 1 the definition of indoor space is provided and indoor navigation requirements are analysed. Section 2 describes the processes of indoor space modeling, as well as routing applications. In Section 3, a case study is examined involving a 3D building model generated in CityEngine (exterior shell) and ArcScene (interior parts), in which the use of commercially available software tools (ArcGIS, ESRI), in terms of indoor routing and 3D network analysis, are explored. The fundamentals of performing 3D analysis with the ArcGIS Network Analyst extension were tested. Finally a geoprocessing model was presented, which was specifically designed to be used to interactively find the best route in ArcScene. The paper ends with discussion and concluding remarks on Section 4.

  18. 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.

  19. Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT1 and ETA receptor antagonists

    PubMed Central

    Singh, Khuraijam Dhanachandra; Muthusamy, Karthikeyan

    2013-01-01

    Aim: Both endothelin ETA receptor antagonists and angiotensin AT1 receptor antagonists lower blood pressure in hypertensive patients. A dual AT1 and ETA receptor antagonist may be more efficacious antihypertensive drug. In this study we identified the mode and mechanism of binding of imidazole series of compounds as dual AT1 and ETA receptor antagonists. Methods: Molecular modeling approach combining quantum-polarized ligand docking (QPLD), MM/GBSA free-energy calculation and 3D-QSAR analysis was used to evaluate 24 compounds as dual AT1 and ETA receptor antagonists and to reveal their binding modes and structural basis of the inhibitory activity. Pharmacophore-based virtual screening and docking studies were performed to identify more potent dual antagonists. Results: 3D-QSAR models of the imidazole compounds were developed from the conformer generated by QPLD, and the resulting models showed a good correlation between the predicted and experimental activity. The visualization of the 3D-QSAR model in the context of the compounds under study revealed the details of the structure-activity relationship: substitution of methoxymethyl and cyclooctanone might increase the activity against AT1 receptor, while substitution of cyclohexone and trimethylpyrrolidinone was important for the activity against ETA receptor; addition of a trimethylpyrrolidinone to compound 9 significantly reduced its activity against AT1 receptor but significantly increased its activity against ETA receptor, which was likely due to the larger size and higher intensities of the H-bond donor and acceptor regions in the active site of ETA receptor. Pharmacophore-based virtual screening followed by subsequent Glide SP, XP, QPLD and MM/GBSA calculation identified 5 potential lead compounds that might act as dual AT1 and ETA receptor antagonists. Conclusion: This study may provide some insights into the development of novel potent dual ETA and AT1 receptor antagonists. As a result, five compounds are

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

    PubMed Central

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

    2008-01-01

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

  1. 3D face analysis for demographic biometrics

    SciTech Connect

    Tokola, Ryan A; Mikkilineni, Aravind K; Boehnen, Chris Bensing

    2015-01-01

    Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and race classification.

  2. 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

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Tavani, Stefano; Corradetti, Amerigo; Billi, Andrea

    2016-05-01

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

  5. A 3D image analysis tool for SPECT imaging

    NASA Astrophysics Data System (ADS)

    Kontos, Despina; Wang, Qiang; Megalooikonomou, Vasileios; Maurer, Alan H.; Knight, Linda C.; Kantor, Steve; Fisher, Robert S.; Simonian, Hrair P.; Parkman, Henry P.

    2005-04-01

    We have developed semi-automated and fully-automated tools for the analysis of 3D single-photon emission computed tomography (SPECT) images. The focus is on the efficient boundary delineation of complex 3D structures that enables accurate measurement of their structural and physiologic properties. We employ intensity based thresholding algorithms for interactive and semi-automated analysis. We also explore fuzzy-connectedness concepts for fully automating the segmentation process. We apply the proposed tools to SPECT image data capturing variation of gastric accommodation and emptying. These image analysis tools were developed within the framework of a noninvasive scintigraphic test to measure simultaneously both gastric emptying and gastric volume after ingestion of a solid or a liquid meal. The clinical focus of the particular analysis was to probe associations between gastric accommodation/emptying and functional dyspepsia. Employing the proposed tools, we outline effectively the complex three dimensional gastric boundaries shown in the 3D SPECT images. We also perform accurate volume calculations in order to quantitatively assess the gastric mass variation. This analysis was performed both with the semi-automated and fully-automated tools. The results were validated against manual segmentation performed by a human expert. We believe that the development of an automated segmentation tool for SPECT imaging of the gastric volume variability will allow for other new applications of SPECT imaging where there is a need to evaluate complex organ function or tumor masses.

  6. Axonemal radial spokes: 3D structure, function and assembly.

    PubMed

    Pigino, Gaia; Ishikawa, Takashi

    2012-02-01

    The radial spoke (RS) is a complex of at least 23 proteins that works as a mechanochemical transducer between the central-pair apparatus and the peripheral microtubule doublets in eukaryotic flagella and motile cilia. The RS contributes to the regulation of the activity of dynein motors, and thus to flagellar motility. Despite numerous biochemical, physiological and structural studies, the mechanism of the function of the radial spoke remains unclear. Detailed knowledge of the 3D structure of the RS protein complex is needed in order to understand how RS regulates dynein activity. Here we review the most important findings on the structure of the RS, including results of our recent cryo-electron tomographic analysis of the RS protein complex. PMID:22754630

  7. 3D Guided Wave Motion Analysis on Laminated Composites

    NASA Technical Reports Server (NTRS)

    Tian, Zhenhua; Leckey, Cara; Yu, Lingyu

    2013-01-01

    Ultrasonic guided waves have proved useful for structural health monitoring (SHM) and nondestructive evaluation (NDE) due to their ability to propagate long distances with less energy loss compared to bulk waves and due to their sensitivity to small defects in the structure. Analysis of actively transmitted ultrasonic signals has long been used to detect and assess damage. However, there remain many challenging tasks for guided wave based SHM due to the complexity involved with propagating guided waves, especially in the case of composite materials. The multimodal nature of the ultrasonic guided waves complicates the related damage analysis. This paper presents results from parallel 3D elastodynamic finite integration technique (EFIT) simulations used to acquire 3D wave motion in the subject laminated carbon fiber reinforced polymer composites. The acquired 3D wave motion is then analyzed by frequency-wavenumber analysis to study the wave propagation and interaction in the composite laminate. The frequency-wavenumber analysis enables the study of individual modes and visualization of mode conversion. Delamination damage has been incorporated into the EFIT model to generate "damaged" data. The potential for damage detection in laminated composites is discussed in the end.

  8. ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.

    PubMed

    Waleń, Tomasz; Chojnowski, Grzegorz; Gierski, Przemysław; Bujnicki, Janusz M

    2014-10-29

    The understanding of folding and function of RNA molecules depends on the identification and classification of interactions between ribonucleotide residues. We developed a new method named ClaRNA for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base-phosphate and base-ribose interactions. The accuracy of ClaRNA is 0.997 for canonical base pairs, 0.983 for non-canonical pairs and 0.961 for stacking interactions. The generalized squared correlation coefficient (GC2) for ClaRNA is 0.969 for canonical base pairs, 0.638 for non-canonical pairs and 0.824 for stacking interactions. The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues. ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules.

  9. 3D-Fun: predicting enzyme function from structure.

    PubMed

    von Grotthuss, Marcin; Plewczynski, Dariusz; Vriend, Gert; Rychlewski, Leszek

    2008-07-01

    The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be annotated with a putative function by comparing them with proteins of known function. This form of annotation is typically performed with BLAST or similar software. Structural genomics is nowadays also bringing us three dimensional structures of proteins with unknown function. We present here software that can be used when sequence comparisons fail to determine the function of a protein with known structure but unknown function. The software, called 3D-Fun, is implemented as a server that runs at several European institutes and is freely available for everybody at all these sites. The 3D-Fun servers accept protein coordinates in the standard PDB format and compare them with all known protein structures by 3D structural superposition using the 3D-Hit software. If structural hits are found with proteins with known function, these are listed together with their function and some vital comparison statistics. This is conceptually very similar in 3D to what BLAST does in 1D. Additionally, the superposition results are displayed using interactive graphics facilities. Currently, the 3D-Fun system only predicts enzyme function but an expanded version with Gene Ontology predictions will be available soon. The server can be accessed at http://3dfun.bioinfo.pl/ or at http://3dfun.cmbi.ru.nl/.

  10. Automated RNA 3D Structure Prediction with RNAComposer.

    PubMed

    Biesiada, Marcin; Purzycka, Katarzyna J; Szachniuk, Marta; Blazewicz, Jacek; Adamiak, Ryszard W

    2016-01-01

    RNAs adopt specific structures to perform their activities and these are critical to virtually all RNA-mediated processes. Because of difficulties in experimentally assessing structures of large RNAs using NMR, X-ray crystallography, or cryo-microscopy, there is currently great demand for new high-resolution 3D structure prediction methods. Recently we reported on RNAComposer, a knowledge-based method for the fully automated RNA 3D structure prediction from a user-defined secondary structure. RNAComposer method is especially suited for structural biology users. Since our initial report in 2012, both servers, freely available at http://rnacomposer.ibch.poznan.pl and http://rnacomposer.cs.put.poznan.pl have been often visited. Therefore this chapter provides guidance for using RNAComposer and discusses points that should be considered when predicting 3D RNA structure. An application example presents current scope and limitations of RNAComposer. PMID:27665601

  11. Source inversion analysis of the 2011 Tohoku-Oki earthquake using Green's functions calculated from a 3-D heterogeneous structure model

    NASA Astrophysics Data System (ADS)

    Suzuki, W.; Aoi, S.; Maeda, T.; Sekiguchi, H.; Kunugi, T.

    2013-12-01

    Source inversion analysis using near-source strong-motion records with an assumption of 1-D underground structure models has revealed the overall characteristics of the rupture process of the 2011 Tohoku-Oki mega-thrust earthquake. This assumption for the structure model is acceptable because the seismic waves radiated during the Tohoku-Oki event were rich in the very-low-frequency contents lower than 0.05 Hz, which are less affected by the small-scale heterogeneous structure. The analysis using more reliable Green's functions even in the higher-frequency range considering complex structure of the subduction zone will illuminate more detailed rupture process in space and time and the transition of the frequency dependence of the wave radiation for the Tohoku-Oki earthquake. In this study, we calculate the near-source Green's functions using a 3-D underground structure model and perform the source inversion analysis using them. The 3-D underground structure model used in this study is the Japan Integrated Velocity Structure Model (Headquarters for Earthquake Research Promotion, 2012). A curved fault model on the Pacific plate interface is discretized into 287 subfaults at ~20 km interval. The Green's functions are calculated using GMS (Aoi et al., 2004), which is a simulation program package for the seismic wave field by the finite difference method using discontinuous grids (Aoi and Fujiwara, 1999). Computational region is 136-146.2E in longitude, 34-41.6N in latitude, and 0-100 km in depth. The horizontal and vertical grid intervals are 200 m and 100 m, respectively, for the shallower region and those for the deeper region are tripled. The number of the total grids is 2.1 billion. We derive 300-s records by calculating 36,000 steps with a time interval of 0.0083 second (120 Hz sampling). It takes nearly one hour to compute one case using 48 Graphics Processing Units (GPU) on TSUBAME2.0 supercomputer owned by Tokyo Institute of Technology. In total, 574 cases are

  12. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  13. 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.

  14. 3D Shape and Indirect Appearance by Structured Light Transport.

    PubMed

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

    2016-07-01

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

  15. 3D joint dynamics analysis of healthy children's gait.

    PubMed

    Samson, William; Desroches, Guillaume; Cheze, Laurence; Dumas, Raphaël

    2009-11-13

    The 3D joint moments and 2D joint powers have been largely explored in the literature of healthy children's gait, in particular to compare them with pathologic subjects' gait. However, no study reported on 3D joint power in children which could be due to the difficulties in interpreting the results. Recently, the analysis of the 3D angle between the joint moment and the joint angular velocity vectors has been proposed in order to help 3D joint power interpretation. Our hypothesis is that this 3D angle may help in characterizing the level of gait maturation. The present study explores 3D joint moments, 3D joint power and the proposed 3D angle for both children's and adults' gaits to highlight differences in the strategies used. The results seem to confirm that children have an alternative strategy of mainly ankle stabilization and hip propulsion compared to the adults' strategy of mainly ankle resistance and propulsion and hip stabilization. In the future, the same 3D angle analysis should be applied to different age groups for better describing the evolution of the 3D joint dynamic strategies during the growth.

  16. The 3D inelastic analysis methods for hot section components

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Maffeo, R. J.; Tipton, M. T.; Weber, G.

    1992-01-01

    A two-year program to develop advanced 3D inelastic structural stress analysis methods and solution strategies for more accurate and cost effective analysis of combustors, turbine blades, and vanes is described. The approach was to develop a matrix of formulation elements and constitutive models. Three constitutive models were developed in conjunction with optimized iterating techniques, accelerators, and convergence criteria within a framework of dynamic time incrementing. Three formulation models were developed: an eight-noded midsurface shell element; a nine-noded midsurface shell element; and a twenty-noded isoparametric solid element. A separate computer program has been developed for each combination of constitutive model-formulation model. Each program provides a functional stand alone capability for performing cyclic nonlinear structural analysis. In addition, the analysis capabilities incorporated into each program can be abstracted in subroutine form for incorporation into other codes or to form new combinations.

  17. On 3D inelastic analysis methods for hot section components

    NASA Technical Reports Server (NTRS)

    Mcknight, R. L.; Chen, P. C.; Dame, L. T.; Holt, R. V.; Huang, H.; Hartle, M.; Gellin, S.; Allen, D. H.; Haisler, W. E.

    1986-01-01

    Accomplishments are described for the 2-year program, to develop advanced 3-D inelastic structural stress analysis methods and solution strategies for more accurate and cost effective analysis of combustors, turbine blades and vanes. The approach was to develop a matrix of formulation elements and constitutive models. Three constitutive models were developed in conjunction with optimized iterating techniques, accelerators, and convergence criteria within a framework of dynamic time incrementing. Three formulations models were developed; an eight-noded mid-surface shell element, a nine-noded mid-surface shell element and a twenty-noded isoparametric solid element. A separate computer program was developed for each combination of constitutive model-formulation model. Each program provides a functional stand alone capability for performing cyclic nonlinear structural analysis. In addition, the analysis capabilities incorporated into each program can be abstracted in subroutine form for incorporation into other codes or to form new combinations.

  18. Assembly of graphene sheets into 3D macroscopic structures.

    PubMed

    Yin, Shengyan; Niu, Zhiqiang; Chen, Xiaodong

    2012-08-20

    Integration of graphene sheets, 2D nanoscale building blocks, into 3D macroscopic assemblies and ultimately into a functional system is essential to explore the advanced properties of individual graphene sheets for macroscopic applications. This Concept paper summarizes different ways, such as flow-directed assembly, layer-by-layer deposition, template-directed method, and leavening strategy to assemble graphene sheets into the layered and porous 3D macroscopic structures. The obtained structures show unique properties, such as flexible network, high specific surface area, and outstanding electrical and mechanical properties. Furthermore, the functional systems based on such graphene 3D macroscopic structures have shown enhanced performance in the applications of energy storage, catalysis, environmental remediation, and sensing.

  19. Influence of material property variability on the mechanical behaviour of carotid atherosclerotic plaques: a 3D fluid-structure interaction analysis.

    PubMed

    Yuan, Jianmin; Teng, Zhongzhao; Feng, Jiaxuan; Zhang, Yongxue; Brown, Adam J; Gillard, Jonathan H; Jing, Zaiping; Lu, Qingsheng

    2015-08-01

    Mechanical analysis has been shown to be complementary to luminal stenosis in assessing atherosclerotic plaque vulnerability. However, patient-specific material properties are not available and the effect of material properties variability has not been fully quantified. Media and fibrous cap (FC) strips from carotid endarterectomy samples were classified into hard, intermediate and soft according to their incremental Young's modulus. Lipid and intraplaque haemorrhage/thrombus strips were classified as hard and soft. Idealised geometry-based 3D fluid-structure interaction analyses were performed to assess the impact of material property variability in predicting maximum principal stress (Stress-P1 ) and stretch (Stretch-P1 ). When FC was thick (1000 or 600 µm), Stress-P1 at the shoulder was insensitive to changes in material stiffness, whereas Stress-P1 at mid FC changed significantly. When FC was thin (200 or 65 µm), high stress concentrations shifted from the shoulder region to mid FC, and Stress-P1 became increasingly sensitive to changes in material properties, in particular at mid FC. Regardless of FC thickness, Stretch-P1 at these locations was sensitive to changes in material properties. Variability in tissue material properties influences both the location and overall stress/stretch value. This variability needs to be accounted for when interpreting the results of mechanical modelling. PMID:25940741

  20. Influence of material property variability on the mechanical behaviour of carotid atherosclerotic plaques: a 3D fluid-structure interaction analysis.

    PubMed

    Yuan, Jianmin; Teng, Zhongzhao; Feng, Jiaxuan; Zhang, Yongxue; Brown, Adam J; Gillard, Jonathan H; Jing, Zaiping; Lu, Qingsheng

    2015-08-01

    Mechanical analysis has been shown to be complementary to luminal stenosis in assessing atherosclerotic plaque vulnerability. However, patient-specific material properties are not available and the effect of material properties variability has not been fully quantified. Media and fibrous cap (FC) strips from carotid endarterectomy samples were classified into hard, intermediate and soft according to their incremental Young's modulus. Lipid and intraplaque haemorrhage/thrombus strips were classified as hard and soft. Idealised geometry-based 3D fluid-structure interaction analyses were performed to assess the impact of material property variability in predicting maximum principal stress (Stress-P1 ) and stretch (Stretch-P1 ). When FC was thick (1000 or 600 µm), Stress-P1 at the shoulder was insensitive to changes in material stiffness, whereas Stress-P1 at mid FC changed significantly. When FC was thin (200 or 65 µm), high stress concentrations shifted from the shoulder region to mid FC, and Stress-P1 became increasingly sensitive to changes in material properties, in particular at mid FC. Regardless of FC thickness, Stretch-P1 at these locations was sensitive to changes in material properties. Variability in tissue material properties influences both the location and overall stress/stretch value. This variability needs to be accounted for when interpreting the results of mechanical modelling.

  1. 3D printing of nano- and micro-structures

    NASA Astrophysics Data System (ADS)

    Ramasamy, Mouli; Varadan, Vijay K.

    2016-04-01

    Additive manufacturing or 3D printing techniques are being vigorously investigated as a replacement to the traditional and conventional methods in fabrication to bring forth cost and time effective approaches. Introduction of 3D printing has led to printing micro and nanoscale structures including tissues and organelles, bioelectric sensors and devices, artificial bones and transplants, microfluidic devices, batteries and various other biomaterials. Various microfabrication processes have been developed to fabricate micro components and assemblies at lab scale. 3D Fabrication processes that can accommodate the functional and geometrical requirements to realize complicated structures are becoming feasible through advances in additive manufacturing. This advancement could lead to simpler development mechanisms of novel components and devices exhibiting complex features. For instance, development of microstructure electrodes that can penetrate the epidermis of the skin to collect the bio potential signal may prove very effective than the electrodes that measure signal from the skin's surface. The micro and nanostructures will have to possess extraordinary material and mechanical properties for its dexterity in the applications. A substantial amount of research being pursued on stretchable and flexible devices based on PDMA, textiles, and organic electronics. Despite the numerous advantages these substrates and techniques could solely offer, 3D printing enables a multi-dimensional approach towards finer and complex applications. This review emphasizes the use of 3D printing to fabricate micro and nanostructures for that can be applied for human healthcare.

  2. 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

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

    PubMed

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

    2016-07-01

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

  4. The 3D structure of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Patsourakos, Spiros

    2016-07-01

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

  5. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  6. 3D Vegetation Structure Extraction from Lidar Remote Sensing

    NASA Astrophysics Data System (ADS)

    Ni-Meister, W.

    2006-05-01

    Vegetation structure data are critical not only for biomass estimation and global carbon cycle studies, but also for ecosystem disturbance, species habitat and ecosystem biodiversity studies. However those data are rarely available at the global scale. Multispectral passive remote sensing has shown little success on this direction. The upcoming lidar remote sensing technology shows a great potential to measure vegetation vertical structure data globally. In this study, we present and test a Bayesian Stochastic Inversion (BSI) approach to invert a full canopy Geometric Optical and Radiative Transfer (GORT) model to retrieve 3-D vegetation structure parameters from large footprint (15m-25m diameter) vegetation lidar data. BSI approach allows us to take into account lidar-directly derived structure parameters, such as tree height and the upper and lower bounds of crown height and their uncertainties as the prior knowledge in the inversion. It provides not only the optimal estimates of model parameters, but also their uncertainties. We first assess the accuracy of vegetation structure parameter retrievals from vegetation lidar data through a comprehensive GORT input parameter sensitivity analysis. We calculated the singular value decomposition (SVD) of Jacobian matrix, which contains the partial derivatives of the combined model with respect to all relevant model input parameters and. Our analysis shows that with the prior knowledge of tree height, crown depth and crown shape, lidar waveforms is most sensitive to the tree density, then to the tree size and the least to the foliage area volume density. It indicates that tree density can be retrieved with the most accuracy and then the tree size, the least is the foliage area volume density. We also test the simplified BSI approach through a synthetic experiment. The synthetic lidar waveforms were generated based the vegetation structure data obtained from the Boreal Ecosystem Atmosphere Study (BOREAS). With the exact

  7. 3D Soil Images Structure Quantification using Relative Entropy

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  8. 3D Structure of the Dihydropyridine Receptor of Skeletal Muscle.

    PubMed

    Samsó, Montserrat

    2015-01-01

    Excitation contraction coupling, the rapid and massive Ca(2+) release under control of an action potential that triggers muscle contraction, takes places at specialized regions of the cell called triad junctions. There, a highly ordered supramolecular complex between the dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) mediates the quasi-instantaneous conversion from T-tubule depolarization into Ca(2+) release from the sarcoplasmic reticulum (SR). The DHPR has several key modules required for EC coupling: the voltage sensors and II-III loop in the alpha1s subunit, and the beta subunit. To gain insight into their molecular organization, this review examines the most updated 3D structure of the DHPR as obtained by transmission electron microscopy and image reconstruction. Although structure determination of a heteromeric membrane protein such as the DHPR is challenging, novel technical advances in protein expression and 3D labeling facilitated this task. The 3D structure of the DHPR complex consists of a main body with five irregular corners around its perimeter encompassing the transmembrane alpha 1s subunit besides the intracellular beta subunit, an extended extracellular alpha 2 subunit, and a bulky intracellular II-III loop. The structural definition attained at 19 Å resolution enabled docking of the atomic coordinates of structural homologs of the alpha1s and beta subunits. These structural features, together with their relative location with respect to the RyR1, are discussed in the context of the functional data. PMID:26913147

  9. Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 2. Application of the novel 3D molecular descriptors to QSAR/QSPR studies.

    PubMed

    Consonni, Viviana; Todeschini, Roberto; Pavan, Manuela; Gramatica, Paola

    2002-01-01

    In a previous paper the theory of the new molecular descriptors called GETAWAY (GEometry, Topology, and Atom-Weights AssemblY) was explained. These descriptors have been proposed with the aim of matching 3D-molecular geometry, atom relatedness, and chemical information. In this paper prediction ability in structure-property correlations of GETAWAY descriptors has been tested extensively by analyzing the regressions of these descriptors for selected properties of some reference compound classes. Moreover, the general performance of the new descriptors in QSAR/QSPR has been evaluated with respect to other well-known sets of molecular descriptors.

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

    PubMed

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

    2015-07-29

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

  11. 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

  12. Formation of coherent structures in 3D laminar mixing flows

    NASA Astrophysics Data System (ADS)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  13. Gene3D: comprehensive structural and functional annotation of genomes.

    PubMed

    Yeats, Corin; Lees, Jonathan; Reid, Adam; Kellam, Paul; Martin, Nigel; Liu, Xinhui; Orengo, Christine

    2008-01-01

    Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein-protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/ PMID:18032434

  14. 3-D Numerical Modeling of a Complex Salt Structure

    SciTech Connect

    House, L.; Larsen, S.; Bednar, J.B.

    2000-02-17

    Reliably processing, imaging, and interpreting seismic data from areas with complicated structures, such as sub-salt, requires a thorough understanding of elastic as well as acoustic wave propagation. Elastic numerical modeling is an essential tool to develop that understanding. While 2-D elastic modeling is in common use, 3-D elastic modeling has been too computationally intensive to be used routinely. Recent advances in computing hardware, including commodity-based hardware, have substantially reduced computing costs. These advances are making 3-D elastic numerical modeling more feasible. A series of example 3-D elastic calculations were performed using a complicated structure, the SEG/EAGE salt structure. The synthetic traces show that the effects of shear wave propagation can be important for imaging and interpretation of images, and also for AVO and other applications that rely on trace amplitudes. Additional calculations are needed to better identify and understand the complex wave propagation effects produced in complicated structures, such as the SEG/EAGE salt structure.

  15. 3D printed components with ultrasonically arranged microscale structure

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  16. The 3D inelastic analysis methods for hot section components

    NASA Technical Reports Server (NTRS)

    Dame, L. T.; Mcknight, R. L.

    1983-01-01

    The objective of this research is to develop an analytical tool capable of economically evaluating the cyclic time dependent plasticity which occurs in hot section engine components in areas of strain concentration resulting from the combination of both mechanical and thermal stresses. The techniques developed must be capable of accommodating large excursions in temperatures with the associated variations in material properties including plasticity and creep. The overall objective of this proposed program is to develop advanced 3-D inelastic structural/stress analysis methods and solution strategies for more accurate and yet more cost effective analysis of combustors, turbine blades, and vanes. The approach will be to develop four different theories, one linear and three higher order with increasing complexities including embedded singularities.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  18. Slat Cove Unsteadiness Effect of 3D Flow Structures

    NASA Technical Reports Server (NTRS)

    Choudhari, Meelan M.; Khorrami, Mehdi R.

    2006-01-01

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

  19. All dispenser printed flexible 3D structured thermoelectric generators

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  20. Cancer3D: understanding cancer mutations through protein structures

    PubMed Central

    Porta-Pardo, Eduard; Hrabe, Thomas; Godzik, Adam

    2015-01-01

    The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14 700 proteins mapped to more than 24 300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution. PMID:25392415

  1. 3D Structure, Dimerization Modeling, and Lead Discovery by Ligand-protein Interaction Analysis of p60 Transcription Regulator Protein (p60TRP).

    PubMed

    Pramanik, Subrata; Kutzner, Arne; Heese, Klaus

    2016-04-01

    The p60 transcription regulator protein (p60TRP) is a basic helix-loop-helix (bHLH) domain-containing neuroprotective protein and a member of the G-protein-coupled receptor (GPCR)-associated sorting protein (GPRASP) family. In the present study, multiple theoretical physico-chemical methods (e.g. Modeller v.9.13, I-TASSER, PROCHECK and ClusPro v2.0 with PIPER) were applied to unveil the three-dimensional (3D) protein structure of the p60TRP homo-dimer protein and explore potential ligand-protein interactions. Our results suggest a Mg(2+) -containing 3D p60TRP dimer protein that potentially interacts with 5-(1-aziridinyl)-2,4-dinitrobenzamide (CB1954) and [2-(3-dodecylimidazolidin-1-yl)-1-phosphonoethyl] phosphonic acid (B73). The discovery of CB1954 and B73 may serve as a potential lead for further drug screening tests to normalize the p60TRP signaling pathway in neurodegenerative diseases. Interference with p60TRP signaling via CB1954/B73-related molecules might be a novel option for modifying neurodegenerative signaling pathways (e.g. RIN1, PP2A, RanBP5, CREB and SYNJ1) to treat various brain diseases. PMID:27491919

  2. Nanoparticle imaging. 3D structure of individual nanocrystals in solution by electron microscopy.

    PubMed

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

    2015-07-17

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale. PMID:26185247

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  4. Alignment-independent technique for 3D QSAR analysis.

    PubMed

    Wilkes, Jon G; Stoyanova-Slavova, Iva B; Buzatu, Dan A

    2016-04-01

    Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test (2) = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test (2) = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test (2) = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

  5. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets.

    PubMed

    Peng, Hanchuan; Ruan, Zongcai; Long, Fuhui; Simpson, Julie H; Myers, Eugene W

    2010-04-01

    The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects. V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems. To demonstrate this extensibility, we built a V3D-based application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images. V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools. Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain. PMID:20231818

  6. Fabrication of 3-D Submicron Glass Structures by FIB

    NASA Astrophysics Data System (ADS)

    Chao, C. H.; Shen, S. C.; Wu, J. R.

    2009-10-01

    The fabrication characteristic of focused ion beam (FIB) for Pyrex glass was investigated. FIB has several advantages such as high resolution, high material removal rates, low forward scattering, and direct fabrication in selective area without any etching mask. In this study, FIB-etched Pyrex glass was used for fast fabrication of 3-D submicron structures. A glass structure with 0.39 μm in width was fabricated. The experimental results in terms of limiting beam size, ion dose (ion/cm2), and beam current are discussed. The influence of XeF2 gas on FIB glass fabrication was investigated.

  7. 3D lidar imaging for detecting and understanding plant responses and canopy structure.

    PubMed

    Omasa, Kenji; Hosoi, Fumiki; Konishi, Atsumi

    2007-01-01

    Understanding and diagnosing plant responses to stress will benefit greatly from three-dimensional (3D) measurement and analysis of plant properties because plant responses are strongly related to their 3D structures. Light detection and ranging (lidar) has recently emerged as a powerful tool for direct 3D measurement of plant structure. Here the use of 3D lidar imaging to estimate plant properties such as canopy height, canopy structure, carbon stock, and species is demonstrated, and plant growth and shape responses are assessed by reviewing the development of lidar systems and their applications from the leaf level to canopy remote sensing. In addition, the recent creation of accurate 3D lidar images combined with natural colour, chlorophyll fluorescence, photochemical reflectance index, and leaf temperature images is demonstrated, thereby providing information on responses of pigments, photosynthesis, transpiration, stomatal opening, and shape to environmental stresses; these data can be integrated with 3D images of the plants using computer graphics techniques. Future lidar applications that provide more accurate dynamic estimation of various plant properties should improve our understanding of plant responses to stress and of interactions between plants and their environment. Moreover, combining 3D lidar with other passive and active imaging techniques will potentially improve the accuracy of airborne and satellite remote sensing, and make it possible to analyse 3D information on ecophysiological responses and levels of various substances in agricultural and ecological applications and in observations of the global biosphere. PMID:17030540

  8. Computerized analysis of pelvic incidence from 3D images

    NASA Astrophysics Data System (ADS)

    Vrtovec, Tomaž; Janssen, Michiel M. A.; Pernuš, Franjo; Castelein, René M.; Viergever, Max A.

    2012-02-01

    The sagittal alignment of the pelvis can be evaluated by the angle of pelvic incidence (PI), which is constant for an arbitrary subject position and orientation and can be therefore compared among subjects in standing, sitting or supine position. In this study, PI was measured from three-dimensional (3D) computed tomography (CT) images of normal subjects that were acquired in supine position. A novel computerized method, based on image processing techniques, was developed to automatically determine the anatomical references required to measure PI, i.e. the centers of the femoral heads in 3D, and the center and inclination of the sacral endplate in 3D. Multiplanar image reformation was applied to obtain perfect sagittal views with all anatomical structures completely in line with the hip axis, from which PI was calculated. The resulting PI (mean+/-standard deviation) was equal to 46.6°+/-9.2° for male subjects (N = 189), 47.6°+/-10.7° for female subjects (N = 181), and 47.1°+/-10.0° for all subjects (N = 370). The obtained measurements of PI from 3D images were not biased by acquisition projection or structure orientation, because all anatomical structures were completely in line with the hip axis. The performed measurements in 3D therefore represent PI according to the actual geometrical relationships among anatomical structures of the sacrum, pelvis and hips, as observed from the perfect sagittal views.

  9. Automatic structural matching of 3D image data

    NASA Astrophysics Data System (ADS)

    Ponomarev, Svjatoslav; Lutsiv, Vadim; Malyshev, Igor

    2015-10-01

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

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

    SciTech Connect

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

    2004-04-28

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

  11. Automating the determination of 3D protein structure

    SciTech Connect

    Rayl, K.D.

    1993-12-31

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

  12. An endoscopic 3D scanner based on structured light.

    PubMed

    Schmalz, Christoph; Forster, Frank; Schick, Anton; Angelopoulou, Elli

    2012-07-01

    We present a new endoscopic 3D scanning system based on Single Shot Structured Light. The proposed design makes it possible to build an extremely small scanner. The sensor head contains a catadioptric camera and a pattern projection unit. The paper describes the working principle and calibration procedure of the sensor. The prototype sensor head has a diameter of only 3.6mm and a length of 14mm. It is mounted on a flexible shaft. The scanner is designed for tubular cavities and has a cylindrical working volume of about 30mm length and 30mm diameter. It acquires 3D video at 30 frames per second and typically generates approximately 5000 3D points per frame. By design, the resolution varies over the working volume, but is generally better than 200μm. A prototype scanner has been built and is evaluated in experiments with phantoms and biological samples. The recorded average error on a known test object was 92μm.

  13. 3D image analysis of abdominal aortic aneurysm

    NASA Astrophysics Data System (ADS)

    Subasic, Marko; Loncaric, Sven; Sorantin, Erich

    2001-07-01

    In this paper we propose a technique for 3-D segmentation of abdominal aortic aneurysm (AAA) from computed tomography angiography (CTA) images. Output data (3-D model) form the proposed method can be used for measurement of aortic shape and dimensions. Knowledge of aortic shape and size is very important in planning of minimally invasive procedure that is for selection of appropriate stent graft device for treatment of AAA. The technique is based on a 3-D deformable model and utilizes the level-set algorithm for implementation of the method. The method performs 3-D segmentation of CTA images and extracts a 3-D model of aortic wall. Once the 3-D model of aortic wall is available it is easy to perform all required measurements for appropriate stent graft selection. The method proposed in this paper uses the level-set algorithm for deformable models, instead of the classical snake algorithm. The main advantage of the level set algorithm is that it enables easy segmentation of complex structures, surpassing most of the drawbacks of the classical approach. We have extended the deformable model to incorporate the a priori knowledge about the shape of the AAA. This helps direct the evolution of the deformable model to correctly segment the aorta. The algorithm has been implemented in IDL and C languages. Experiments have been performed using real patient CTA images and have shown good results.

  14. 3-D structure and dynamics of microtubule self-organization

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Ou-Yang, H. Daniel

    2008-03-01

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

  15. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  16. 3-D transient analysis of pebble-bed HTGR by TORT-TD/ATTICA3D

    SciTech Connect

    Seubert, A.; Sureda, A.; Lapins, J.; Buck, M.; Bader, J.; Laurien, E.

    2012-07-01

    As most of the acceptance criteria are local core parameters, application of transient 3-D fine mesh neutron transport and thermal hydraulics coupled codes is mandatory for best estimate evaluations of safety margins. This also applies to high-temperature gas cooled reactors (HTGR). Application of 3-D fine-mesh transient transport codes using few energy groups coupled with 3-D thermal hydraulics codes becomes feasible in view of increasing computing power. This paper describes the discrete ordinates based coupled code system TORT-TD/ATTICA3D that has recently been extended by a fine-mesh diffusion solver. Based on transient analyses for the PBMR-400 design, the transport/diffusion capabilities are demonstrated and 3-D local flux and power redistribution effects during a partial control rod withdrawal are shown. (authors)

  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 geophysical investigations of shallow karstic structures

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Genthon, P.; Perroud, H.; Sénéchal, G.

    2003-04-01

    The accurate determination of shallow kastified areas is of major importance for the quantitative modelling of fluid transfer as well as for geotechnical issues. Near surface geophysics offers a broad range of tools dedicated to the study of voids and other cavities filled with water or sediments. We present the results of various geophysical studies (seismics, GPR, 2-D and 3-D DC resitivity) in the Baget area, a hydrologically well monitored zone, in the vicinity of Moulis underground laboratory in the Central Pyrenees. The studied area is a 1Km long segment of a narrow EW valley, located on the boundary between limestones and shales, with emphasis on a 100m long anomalous zone. begin{itemize} Seismics doesn't allow to derive a focused image of the very shallow (< 2m) structure but amplitude anomalies suggest the presence of scattering structures in the valley. GPR data clearly show the sedimentary filling of the valley, overlying the generally transparent limestone basement. Two highly reflective zones evidence the presence of heterogeneities. 2-D DC resistivity exhibits very different results whether the lines are in the direction of the valley or perpendicular to it. Results suggest a strong influence of the topography leading to completely erroneous conclusions without complementary data. The presentation is focused on GPR and DC resitivity methods. The limitations of 3-D DC inversion is partly overcome by transforming the data from pole-pole pattern to dipole-dipole, allowing us to get more details on the shallow and short wavelenght structures with conventional software. Voids are indicated by the presence of a temporary river and speleological exploration but the results of the study show the absence of big cavities under the surface, within the first meters of limestone. GPR and DC resitivity studies reveal the presence of shallow metric heterogeneities which can be the water conduit system. 3-D investigation is necessary to get consistent results.

  19. STEALTH: a Lagrange explicit finite-difference code for solid, structural, and thermohydraulic analysis. Volume 8B. STEALTH/WHAMSE: a 3-D fluid-structure interaction code

    SciTech Connect

    Not Available

    1984-10-01

    STEALTH is a family of computer codes that can be used to calculate a variety of physical processes in which the dynamic behavior of a continuum is involved. The version of STEALTH described in this volume is designed for calculations of fluid-structure interaction. This version of the program consists of a hydrodynamic version of STEALTH which has been coupled to a finite-element code, WHAMSE. STEALTH computes the transient response of the fluid continuum, while WHAMSE computes the transient response of shell and beam structures under external fluid loadings. The coupling between STEALTH and WHAMSE is performed during each cycle or step of a calculation. Separate calculations of fluid response and structure response are avoided, thereby giving a more accurate model of the dynamic coupling between fluid and structure. This volume provides the theoretical background, the finite-difference equations, the finite-element equations, a discussion of several sample problems, a listing of the input decks for the sample problems, a programmer's manual and a description of the input records for the STEALTH/WHAMSE computer program.

  20. Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.

    PubMed

    Lössl, Philip; Sinz, Andrea

    2016-01-01

    During the last 15 years, the combination of chemical cross-linking and high-resolution mass spectrometry (MS) has matured into an alternative approach for analyzing 3D-structures of proteins and protein complexes. Using the distance constraints imposed by the cross-links, models of the protein or protein complex under investigation can be created. The majority of cross-linking studies are currently conducted with homobifunctional amine-reactive cross-linkers. We extend this "traditional" cross-linking/MS strategy by adding complementary photo-cross-linking data. For this, the diazirine-containing unnatural amino acids photo-leucine and photo-methionine are incorporated into the proteins and cross-link formation is induced by UV-A irradiation. The advantage of the photo-cross-linking strategy is that it is not restricted to lysine residues and that hydrophobic regions in proteins can be targeted, which is advantageous for investigating membrane proteins. We consider the strategy of combining cross-linkers with orthogonal reactivities and distances to be ideally suited for maximizing the amount of structural information that can be gained from a cross-linking experiment.

  1. Reducing Non-Uniqueness in Satellite Gravity Inversion using 3D Object Oriented Image Analysis Techniques

    NASA Astrophysics Data System (ADS)

    Fadel, I.; van der Meijde, M.; Kerle, N.

    2013-12-01

    Non-uniqueness of satellite gravity interpretation has been usually reduced by using a priori information from various sources, e.g. seismic tomography models. The reduction in non-uniqueness has been based on velocity-density conversion formulas or user interpretation for 3D subsurface structures (objects) in seismic tomography models. However, these processes introduce additional uncertainty through the conversion relations due to the dependency on the other physical parameters such as temperature and pressure, or through the bias in the interpretation due to user choices and experience. In this research, a new methodology is introduced to extract the 3D subsurface structures from 3D geophysical data using a state-of-art 3D Object Oriented Image Analysis (OOA) technique. 3D OOA is tested using a set of synthetic models that simulate the real situation in the study area of this research. Then, 3D OOA is used to extract 3D subsurface objects from a real 3D seismic tomography model. The extracted 3D objects are used to reconstruct a forward model and its response is compared with the measured satellite gravity. Finally, the result of the forward modelling, based on the extracted 3D objects, is used to constrain the inversion process of satellite gravity data. Through this work, a new object-based approach is introduced to interpret and extract the 3D subsurface objects from 3D geophysical data. This can be used to constrain modelling and inversion of potential field data using the extracted 3D subsurface structures from other methods. In summary, a new approach is introduced to constrain inversion of satellite gravity measurements and enhance interpretation capabilities.

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

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

    PubMed

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

    2016-08-01

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

  4. 3-D structural analysis of the crucial intermediate of skeletal muscle myosin and its role in revised actomyosin cross-bridge cycle

    PubMed Central

    Katayama, Eisaku

    2014-01-01

    Skeletal myosin S1 consists of two functional segments, a catalytic-domain and a lever-arm. Since the crystal structure of ADP/Vi-bound S1 exhibits a strong intramolecular flexure between two segments, inter-conversion between bent and extended forms; i.e. “tilting of the lever-arm” has been accepted as the established molecular mechanism of skeletal muscle contraction. We utilized quick-freeze deep-etch replica electron microscopy to directly visualize the structure of in vitro actin-sliding myosin, and found the existence of a novel oppositely-bent configuration, instead of the expected ADP/Vi-bound form. We also noticed that SH1–SH2 cross-linked myosin gives an aberrant appearance similar to the above structure. Since SH1–SH2-cross-linked myosin is a well-studied analogue of the transient intermediate of the actomyosin cross-bridge cycle, we devised a new image-processing procedure to define the relative view-angles between the catalytic-domain and the lever-arm from those averaged images, and built a 3-D model of the new conformer. The lever-arm in that model was bent oppositely to the ADP/Vi-bound form, in accordance with observed actin-sliding cross-bridge structure. Introducing this conformer as the crucial intermediate that transiently appears during sliding, we propose a revised scheme of the cross-bridge cycle. In the scenario, the novel conformer keeps actin-binding in two different modes until it forms a primed configuration. The final extension of the lever-arm back to the original rigor-state constitutes the “power-stroke”. Various images observed during sliding could be easily interpreted by the new conformer. Even the enigmatic behavior of the cross-bridges reported as “loose chemo-mechanical coupling” might be adequately explained under some assumptions. PMID:27493503

  5. Use of laser 3D surface digitizer in data collection and 3D modeling of anatomical structures

    NASA Astrophysics Data System (ADS)

    Tse, Kelly; Van Der Wall, Hans; Vu, Dzung H.

    2006-02-01

    A laser digitizer (Konica-Minolta Vivid 910) is used to obtain 3-dimensional surface scans of anatomical structures with a maximum resolution of 0.1mm. Placing the specimen on a turntable allows multiple scans allaround because the scanner only captures data from the portion facing its lens. A computer model is generated using 3D modeling software such as Geomagic. The 3D model can be manipulated on screen for repeated analysis of anatomical features, a useful capability when the specimens are rare or inaccessible (museum collection, fossils, imprints in rock formation.). As accurate measurements can be performed on the computer model, instead of taking measurements on actual specimens only at the archeological excavation site e.g., a variety of quantitative data can be later obtained on the computer model in the laboratory as new ideas come to mind. Our group had used a mechanical contact digitizer (Microscribe) for this purpose, but with the surface digitizer, we have been obtaining data sets more accurately and more quickly.

  6. 3D Regression Heat Map Analysis of Population Study Data.

    PubMed

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease. PMID:26529689

  7. 3D Regression Heat Map Analysis of Population Study Data.

    PubMed

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease.

  8. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

    PubMed

    Levashov, V A

    2016-03-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale. PMID:26957166

  9. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors.

    PubMed

    Levashov, V A

    2016-03-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a 3D model binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. This approach allows to interpret correlations relevant to the Green-Kubo expression for viscosity in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonstrate that this behaviour originates from the orientational correlations between the eigenvectors of the atomic stress tensors. We also found correlations between the eigenvalues of the same atomic stress tensor. For the studied system, with purely repulsive interactions between the particles, the eigenvalues of every atomic stress tensor are positive and they can be ordered: λ1 ≥ λ2 ≥ λ3 ≥ 0. We found that, for the particles of a given type, the probability distributions of the ratios (λ2/λ1) and (λ3/λ2) are essentially identical to each other in the liquids state. We also found that λ2 tends to be equal to the geometric average of λ1 and λ3. In our view, correlations between the eigenvalues may represent "the Poisson ratio effect" at the atomic scale.

  10. Structural analysis and implicit 3D modelling of high-grade host rocks to the Venetia kimberlite diatremes, Central Zone, Limpopo Belt, South Africa

    NASA Astrophysics Data System (ADS)

    Basson, I. J.; Creus, P. K.; Anthonissen, C. J.; Stoch, B.; Ekkerd, J.

    2016-05-01

    The Beit Bridge Complex of the Central Zone (CZ) of the Limpopo Belt hosts the 519 ± 6 Ma Venetia kimberlite diatremes. Deformed shelf- or platform-type supracrustal sequences include the Mount Dowe, Malala Drift and Gumbu Groups, comprising quartzofeldspathic units, biotite-bearing gneiss, quartzite, metapelite, metacalcsilicate and ortho- and para-amphibolite. Previous studies define tectonometamorphic events at 3.3-3.1 Ga, 2.7-2.5 Ga and 2.04 Ga. Detailed structural mapping over 10 years highlights four deformation events at Venetia. Rules-based implicit 3D modelling in Leapfrog Geo™ provides an unprecedented insight into CZ ductile deformation and sheath folding. D1 juxtaposed gneisses against metasediments. D2 produced a pervasive axial planar foliation (S2) to isoclinal F2 folds. Sheared lithological contacts and S2 were refolded into regional, open, predominantly southward-verging, E-W trending F3 folds. Intrusion of a hornblendite protolith occurred at high angles to incipient S2. Constrictional-prolate D4 shows moderately NE-plunging azimuths defined by elongated hornblendite lenses, andalusite crystals in metapelite, crenulations in fuchsitic quartzite and sheath folding. D4 overlaps with a: 1) 2.03-2.01 Ga regional M3 metamorphic overprint; b) transpressional deformation at 2.2-1.9 Ga and c) 2.03 Ga transpressional, dextral shearing and thrusting around the CZ and d) formation of the Avoca, Bellavue and Baklykraal sheath folds and parallel lineations.

  11. Structure of the antiviral stavudine using quantum chemical methods: Complete conformational space analysis, 3D potential energy surfaces and solid state simulations

    NASA Astrophysics Data System (ADS)

    Alcolea Palafox, M.; Iza, N.

    2012-11-01

    The molecular structure and energy of the anti-HIV, 2',3'-didehydro-3'-deoxythymidine (D4T, stavudine or Zerit) nucleoside analogue was determined by using MP2, B3LYP and B971 quantum chemical methods. The global minimum was determined through 3D potential energy surfaces (PES). These surfaces were built by rotation of the exocyclic χ, γ and β torsional angles, in steps of 20°, and full optimization of the remaining parameters. As consequence 5832 geometries were final optimized. The search located 25 local minimum, 4 of which are by MP2 within a 2 kcal/mol electronic energy range of the global minimum. The whole conformational parameters as well as P, νmax were analyzed in all the stable conformers. The global minimum by MP2 corresponds to the calculated values of the exocyclic torsional angles: χ = -103.6°, β = 63.8° and γ = 60.6°. The results obtained are in accordance to those found in thymidine and in related anti-HIV nucleoside analogues. The effect of hydration on the two most stable conformers is analyzed by continuous and discrete models up to 20 water molecules. The solid state was also simulated. The dimer forms found in the crystal unit cell were accurately determined and they are in accordance to the X-ray data.

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

    DOEpatents

    Zemla, Adam T.

    2011-09-20

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

  13. Horizontal structure and propagation characteristics of mesospheric gravity waves observed by Antarctic Gravity Wave Imaging/Instrument Network (ANGWIN), using a 3-D spectral analysis technique

    NASA Astrophysics Data System (ADS)

    Matsuda, Takashi S.; Nakamura, Takuji; Murphy, Damian; Tsutsumi, Masaki; Moffat-Griffin, Tracy; Zhao, Yucheng; Pautet, Pierre-Dominique; Ejiri, Mitsumu K.; Taylor, Michael

    2016-07-01

    ANGWIN (Antarctic Gravity Wave Imaging/Instrument Network) is an international airglow imager/instrument network in the Antarctic, which commenced observations in 2011. It seeks to reveal characteristics of mesospheric gravity waves, and to study sources, propagation, breaking of the gravity waves over the Antarctic and the effects on general circulation and upper atmosphere. In this study, we compared distributions of horizontal phase velocity of the gravity waves at around 90 km altitude observed in the mesospheric airglow imaging over different locations using our new statistical analysis method of 3-D Fourier transform, developed by Matsuda et al. (2014). Results from the airglow imagers at four stations at Syowa (69S, 40E), Halley (76S, 27W), Davis (69S, 78E) and McMurdo (78S, 156E) out of the ANGWIN imagers have been compared, for the observation period between April 6 and May 21 in 2013. In addition to the horizontal distribution of propagation and phase speed, gravity wave energies have been quantitatively compared, indicating a smaller GW activity in higher latitude stations. We further investigated frequency dependence of gravity wave propagation direction, as well as nightly variation of the gravity wave direction and correlation with the background wind variations. We found that variation of propagation direction is partly due to the effect of background wind in the middle atmosphere, but variation of wave sources could play important role as well. Secondary wave generation is also needed to explain the observed results.

  14. Verification of the NIKE3D structural analysis code by comparison against the analytic solution for a spherical cavity under a far-field uniaxial stress

    SciTech Connect

    Kansa, E.J.

    1989-01-01

    The original scope of this task was to simulate the stresses and displacements of a hard rock tunnel experimental design using a suitable three-dimensional finite element code. NIKE3D was selected as a suitable code for performing these primarily approximate linearly elastic 3D analyses, but it required modifications to include initial stress, shear traction boundary condition and excavation options. During the summer of 1988, such capabilities were installed in a special version of NIKE3D. Subsequently, we verified both the LLNL's commonly used version of NIKE3D and our private modified version against the analytic solution for a spherical cavity in an elastic material deforming under a far-field uniaxial stress. We find the results produced by the unmodified and modified versions of NIKE3D to be in good agreement with the analytic solutions, except near the cavity, where the errors in the stress field are large. As can be expected from a code based on a displacement finite element formulation, the displacements are much more accurate than the stresses calculated from the 8-noded brick elements. To reduce these errors to acceptable levels, the grid must be refined further near the cavity wall. The level of grid refinement required to simulate accurately tunneling problems that do not have spatial symmetry in three dimensions using the current NIKE3D code is likely to exceed the memory capacity of the largest CRAY 1 computers at LLNL. 8 refs., 121 figs.

  15. Dual multispectral and 3D structured light laparoscope

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  16. 3-D Experimental Fracture Analysis at High Temperature

    SciTech Connect

    John H. Jackson; Albert S. Kobayashi

    2001-09-14

    T*e, which is an elastic-plastic fracture parameter based on incremental theory of plasticity, was determined numerically and experimentally. The T*e integral of a tunneling crack in 2024-T3 aluminum, three point bend specimen was obtained through a hybrid analysis of moire interferometry and 3-D elastic-plastic finite element analysis. The results were verified by the good agreement between the experimentally and numerically determined T*e on the specimen surface.

  17. 3-D multi-observable probabilistic inversion for the compositional and thermal structure of the lithosphere and upper mantle. II: General methodology and resolution analysis

    NASA Astrophysics Data System (ADS)

    Afonso, J. C.; Fullea, J.; Yang, Y.; Connolly, J. A. D.; Jones, A. G.

    2013-04-01

    Here we present a 3-D multi-observable probabilistic inversion method, particularly designed for high-resolution (regional) thermal and compositional mapping of the lithosphere and sub-lithospheric upper mantle that circumvents the problems associated with traditional inversion methods. The key aspects of the method are as follows: (a) it exploits the increasing amount and quality of geophysical datasets; (b) it combines multiple geophysical observables (Rayleigh and Love dispersion curves, body-wave tomography, magnetotelluric, geothermal, petrological, gravity, elevation, and geoid) with different sensitivities to deep/shallow, thermal/compositional anomalies into a single thermodynamic-geophysical framework; (c) it uses a general probabilistic (Bayesian) formulation to appraise the data; (d) no initial model is needed; (e) compositional a priori information relies on robust statistical analyses of a large database of natural mantle samples; and (f) it provides a natural platform to estimate realistic uncertainties. In addition, the modular nature of the method/algorithm allows for incorporating or isolating specific forward operators according to available data. The strengths and limitations of the method are thoroughly explored with synthetic models. It is shown that the a posteriori probability density function (i.e., solution to the inverse problem) satisfactorily captures spatial variations in bulk composition and temperature with high resolution, as well as sharp discontinuities in these fields. Our results indicate that only temperature anomalies of ΔT ⪆150°C and large compositional anomalies of ΔMg# > 3 (or bulk ΔAl2O3 > 1.5) can be expected to be resolved simultaneously when combining high-quality geophysical data. This resolving power is sufficient to explore some long-standing problems regarding the nature and evolution of the lithosphere (e.g., vertical stratification of cratonic mantle, compositional versus temperature signatures in seismic

  18. Structural analysis and implicit 3D modelling of high-grade host rocks to the Venetia kimberlite diatremes, Central Zone, Limpopo Belt, South Africa

    NASA Astrophysics Data System (ADS)

    Basson, I. J.; Creus, P. K.; Anthonissen, C. J.; Stoch, B.; Ekkerd, J.

    2016-05-01

    The Beit Bridge Complex of the Central Zone (CZ) of the Limpopo Belt hosts the 519 ± 6 Ma Venetia kimberlite diatremes. Deformed shelf- or platform-type supracrustal sequences include the Mount Dowe, Malala Drift and Gumbu Groups, comprising quartzofeldspathic units, biotite-bearing gneiss, quartzite, metapelite, metacalcsilicate and ortho- and para-amphibolite. Previous studies define tectonometamorphic events at 3.3-3.1 Ga, 2.7-2.5 Ga and 2.04 Ga. Detailed structural mapping over 10 years highlights four deformation events at Venetia. Rules-based implicit 3D modelling in Leapfrog Geo™ provides an unprecedented insight into CZ ductile deformation and sheath folding. D1 juxtaposed gneisses against metasediments. D2 produced a pervasive axial planar foliation (S2) to isoclinal F2 folds. Sheared lithological contacts and S2 were refolded into regional, open, predominantly southward-verging, E-W trending F3 folds. Intrusion of a hornblendite protolith occurred at high angles to incipient S2. Constrictional-prolate D4 shows moderately NE-plunging azimuths defined by elongated hornblendite lenses, andalusite crystals in metapelite, crenulations in fuchsitic quartzite and sheath folding. D4 overlaps with a: 1) 2.03-2.01 Ga regional M3 metamorphic overprint; b) transpressional deformation at 2.2-1.9 Ga and c) 2.03 Ga transpressional, dextral shearing and thrusting around the CZ and d) formation of the Avoca, Bellavue and Baklykraal sheath folds and parallel lineations.

  19. Edge singularities and structure of the 3-D Williams expansion

    NASA Astrophysics Data System (ADS)

    Apel, Thomas; Leguillon, Dominique; Pester, Cornelia; Yosibash, Zohar

    2008-08-01

    The elastic solution in a vicinity of a re-entrant wedge can be described by a Williams like expansion in terms of powers of the distance to a point on the edge. This expansion has a particular structure due to the invariance of the problem by translation parallel to the edge. We show here that some terms, so-called primary solutions, derive directly from solutions to the 2-D corner problem posed in the orthogonal cross section of the domain. The others, baptized shadow functions, derive of the primary solutions by integration along the axis parallel to the edge. This 3-D Williams expansion is shown to be equivalent to the edge expansion proposed by Costabel et al. [M. Costabel, M. Dauge, Z. Yosibash, A quasidual function method for extracting edge stress intensity functions, SIAM J. Math. Anal. 35 (5) (2004) 1177-1202]. To cite this article: T. Apel et al., C. R. Mecanique 336 (2008).

  20. 3D image analysis of a volcanic deposit

    NASA Astrophysics Data System (ADS)

    de Witte, Y.; Vlassenbroeck, J.; Vandeputte, K.; Dewanckele, J.; Cnudde, V.; van Hoorebeke, L.; Ernst, G.; Jacobs, P.

    2009-04-01

    During the last decades, X-ray micro CT has become a well established technique for non-destructive testing in a wide variety of research fields. Using a series of X-ray transmission images of the sample at different projection angles, a stack of 2D cross-sections is reconstructed, resulting in a 3D volume representing the X-ray attenuation coefficients of the sample. Since the attenuation coefficient of a material depends on its density and atomic number, this volume provides valuable information about the internal structure and composition of the sample. Although much qualitative information can be derived directly from this 3D volume, researchers usually require more quantitative results to be able to provide a full characterization of the sample under investigation. This type of information needs to be retrieved using specialized image processing software. For most samples, it is imperative that this processing is performed on the 3D volume as a whole, since a sequence of 2D cross sections usually forms an inadequate approximation of the actual structure. The complete processing of a volume consists of three sequential steps. First, the volume is segmented into a set of objects. What these objects represent depends on what property of the sample needs to be analysed. The objects can be for instance concavities, dense inclusions or the matrix of the sample. When dealing with noisy data, it might be necessary to filter the data before applying the segmentation. The second step is the separation of connected objects into a set of smaller objects. This is necessary when objects appear to be connected because of the limited resolution and contrast of the scan. Separation can also be useful when the sample contains a network structure and one wants to study the individual cells of the network. The third and last step consists of the actual analysis of the various objects to derive the different parameters of interest. While some parameters require extensive

  1. 3D complex: a structural classification of protein complexes.

    PubMed

    Levy, Emmanuel D; Pereira-Leal, Jose B; Chothia, Cyrus; Teichmann, Sarah A

    2006-11-17

    Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  2. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  3. Multifunctional 3D printing of heterogeneous hydrogel structures

    PubMed Central

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  4. Multifunctional 3D printing of heterogeneous hydrogel structures

    NASA Astrophysics Data System (ADS)

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  5. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-01-01

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing. PMID:27630079

  6. Multifunctional 3D printing of heterogeneous hydrogel structures.

    PubMed

    Nadernezhad, Ali; Khani, Navid; Skvortsov, Gözde Akdeniz; Toprakhisar, Burak; Bakirci, Ezgi; Menceloglu, Yusuf; Unal, Serkan; Koc, Bahattin

    2016-09-15

    Multimaterial additive manufacturing or three-dimensional (3D) printing of hydrogel structures provides the opportunity to engineer geometrically dependent functionalities. However, current fabrication methods are mostly limited to one type of material or only provide one type of functionality. In this paper, we report a novel method of multimaterial deposition of hydrogel structures based on an aspiration-on-demand protocol, in which the constitutive multimaterial segments of extruded filaments were first assembled in liquid state by sequential aspiration of inks into a glass capillary, followed by in situ gel formation. We printed different patterned objects with varying chemical, electrical, mechanical, and biological properties by tuning process and material related parameters, to demonstrate the abilities of this method in producing heterogeneous and multi-functional hydrogel structures. Our results show the potential of proposed method in producing heterogeneous objects with spatially controlled functionalities while preserving structural integrity at the switching interface between different segments. We anticipate that this method would introduce new opportunities in multimaterial additive manufacturing of hydrogels for diverse applications such as biosensors, flexible electronics, tissue engineering and organ printing.

  7. 3D Wilson cycle: structural inheritance and subduction polarity reversals

    NASA Astrophysics Data System (ADS)

    Beaussier, Stephane; Gerya, Taras; Burg, Jean-Pierre

    2016-04-01

    Many orogenies display along-strike variations in their orogenic wedge geometry. For instance, the Alps is an example of lateral changes in the subducting lithosphere polarity. High resolution tomography has shown that the southeast dipping European lithosphere is separated from the northeast dipping Adriatic lithosphere by a narrow transition zone at about the "Judicarian" line (Kissling et al. 2006). The formation of such 3D variations remains conjectural. We investigate the conditions that can spontaneously induce such lithospheric structures, and intend to identify the main parameters controlling their formation and geometry. Using the 3D thermo-mechanical code, I3ELVIS (Gerya and Yuen 2007) we modelled a Wilson cycle starting from a continental lithosphere in an extensional setting resulting in continental breakup and oceanic spreading. At a later stage, divergence is gradually reversed to convergence, which induce subduction of the oceanic lithosphere formed during oceanic spreading. In this model, all lateral and longitudinal structures of the lithospheres are generated self-consistently, and are consequences of the initial continental structure, tectono-magmatic inheritance, and material rheology. Our numerical simulations point out the control of rheological parameters defining the brittle/plastic yielding conditions for the lithosphere. Formation of several opposing domains of opposing subduction polarity is facilitated by wide and weak oceanic lithospheres. Furthermore, contrasts of strength between the continental and oceanic lithosphere, as well as the angle between the plate suture and the shortening direction have a second order effect on the lateral geometry of the subduction zone. In our numerical experiments systematic lateral changes in the subduction lithosphere polarity during subduction initiation form spontaneously suggesting intrinsic physical origin of this phenomenon. Further studies are necessary to understand why this feature, observed

  8. 3D printing technology using high viscous materials - Synthesis of functional materials and fabrication of 3D metal structure

    NASA Astrophysics Data System (ADS)

    Hong, Seongik

    In the 3D printing technology, the research for using various materials has been performing. In this research work, 3D printable high viscous materials are suggested as one of the solutions for problems in the traditional 3D printing technology. First, Cu-Ag coreshell was synthesized as a functional material. In terms of the reaction rate, reaction rate limiting step was defined as a fundamental research, and then prepared Cu-Ag coreshell was printed and analyzed. Second, the high viscous Cu paste was prepared and then metal 3D printed structure was fabricated by using new printing method. In the synthesis of Cu-Ag coreshell, different sizes of Cu particle, 2μm and 100nm were used, and when 2μm Cu was applied, the reaction rate was limited by film diffusion control. However, when 100nm Cu was applied, reaction rate was controlled by CuO film and the rate of the reaction, which includes removing CuO film in the solution, is limited by chemical reaction control. The shape of Cu-Ag particle is spherical in the 2μm Cu condition and dendrite shape in the 100nm Cu condition respectively. The conductivity of Cu-Ag coreshell paste increased as increasing content of coreshell particle in the paste and sintering temperature. In order to print high viscous metal paste, the high viscous Cu paste was printed by using screw extruder, and the viscosity of Cu paste was measured as a fundamental research. As increasing wt.% of Cu in the paste, the viscosity also increased. In addition, the shrinkage factor was reduced by increasing wt.% of Cu in the paste. An optimized printing condition for the high viscous material was obtained, and by using this condition, 3D metal structure was fabricated. The final product was heat treated and polished. Through these processes, a fine quality of metal 3D structure was printed.

  9. Simplified Deformation Analysis of 3D-body by First Order Analysis

    NASA Astrophysics Data System (ADS)

    Ali Khan, Md. Shawkut; Yamazaki, Koetsu; Oda, Kosuke; Hirooka, Kazuhiko

    This paper proposes a simplified analysis model of complex solid structure for three-dimensional bodies (3D-bodies) in the First Order Analysis (FOA). A simplified finite element composed of the beam elements is suggested for the deformation analysis of 3D-bodies by extending concept of conforming beam element for the finite element method (FEM). When a complex solid structure is simplified to an assemblage of simple elements applied element forces such as axial forces, shear forces, bending moments as well as twisting moments, the total stiffness equation for the FOA of the solid structure is constructed approximately and solved for the given boundary and loading conditions by the usual manner of the FEM. Then, the total deformation of the complex structure is estimated by the simplified model and the element forces are calculated in the element level. It is found that the finite element analysis via developed simplified element analysis can estimate deformations of complex 3D-bodies in a rational precision, and the results of the analysis are useful for considering the load transmitting path of the structure and for designing a better structure by changing the stiffness of structural components.

  10. 3D Imaging with Structured Illumination for Advanced Security Applications

    SciTech Connect

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

    2015-09-01

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

  11. An Efficient 3D Imaging using Structured Light Systems

    NASA Astrophysics Data System (ADS)

    Lee, Deokwoo

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

  12. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  13. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

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

  14. 3D fluid-structure modelling and vibration analysis for fault diagnosis of Francis turbine using multiple ANN and multiple ANFIS

    NASA Astrophysics Data System (ADS)

    Saeed, R. A.; Galybin, A. N.; Popov, V.

    2013-01-01

    This paper discusses condition monitoring and fault diagnosis in Francis turbine based on integration of numerical modelling with several different artificial intelligence (AI) techniques. In this study, a numerical approach for fluid-structure (turbine runner) analysis is presented. The results of numerical analysis provide frequency response functions (FRFs) data sets along x-, y- and z-directions under different operating load and different position and size of faults in the structure. To extract features and reduce the dimensionality of the obtained FRF data, the principal component analysis (PCA) has been applied. Subsequently, the extracted features are formulated and fed into multiple artificial neural networks (ANN) and multiple adaptive neuro-fuzzy inference systems (ANFIS) in order to identify the size and position of the damage in the runner and estimate the turbine operating conditions. The results demonstrated the effectiveness of this approach and provide satisfactory accuracy even when the input data are corrupted with certain level of noise.

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

    PubMed

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

    2014-07-01

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

  16. Proton-detected 3D 1H/13C/1H correlation experiment for structural analysis in rigid solids under ultrafast-MAS above 60 kHz

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-10-01

    A proton-detected 3D 1H/13C/1H chemical shift correlation experiment is proposed for the assignment of chemical shift resonances, identification of 13C-1H connectivities, and proximities of 13C-1H and 1H-1H nuclei under ultrafast magic-angle-spinning (ultrafast-MAS) conditions. Ultrafast-MAS is used to suppress all anisotropic interactions including 1H-1H dipolar couplings, while the finite-pulse radio frequency driven dipolar recoupling (fp-RFDR) pulse sequence is used to recouple dipolar couplings among protons and the insensitive nuclei enhanced by polarization transfer technique is used to transfer magnetization between heteronuclear spins. The 3D experiment eliminates signals from non-carbon-bonded protons and non-proton-bonded carbons to enhance spectral resolution. The 2D (F1/F3) 1H/1H and 2D 13C/1H (F2/F3) chemical shift correlation spectra extracted from the 3D spectrum enable the identification of 1H-1H proximity and 13C-1H connectivity. In addition, the 2D (F1/F2) 1H/13C chemical shift correlation spectrum, incorporated with proton magnetization exchange via the fp-RFDR recoupling of 1H-1H dipolar couplings, enables the measurement of proximities between 13C and even the remote non-carbon-bonded protons. The 3D experiment also gives three-spin proximities of 1H-1H-13C chains. Experimental results obtained from powder samples of L-alanine and L-histidine ṡ H2O ṡ HCl demonstrate the efficiency of the 3D experiment.

  17. Proton-detected 3D (1)H/(13)C/(1)H correlation experiment for structural analysis in rigid solids under ultrafast-MAS above 60 kHz.

    PubMed

    Zhang, Rongchun; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-10-28

    A proton-detected 3D (1)H/(13)C/(1)H chemical shift correlation experiment is proposed for the assignment of chemical shift resonances, identification of (13)C-(1)H connectivities, and proximities of (13)C-(1)H and (1)H-(1)H nuclei under ultrafast magic-angle-spinning (ultrafast-MAS) conditions. Ultrafast-MAS is used to suppress all anisotropic interactions including (1)H-(1)H dipolar couplings, while the finite-pulse radio frequency driven dipolar recoupling (fp-RFDR) pulse sequence is used to recouple dipolar couplings among protons and the insensitive nuclei enhanced by polarization transfer technique is used to transfer magnetization between heteronuclear spins. The 3D experiment eliminates signals from non-carbon-bonded protons and non-proton-bonded carbons to enhance spectral resolution. The 2D (F1/F3) (1)H/(1)H and 2D (13)C/(1)H (F2/F3) chemical shift correlation spectra extracted from the 3D spectrum enable the identification of (1)H-(1)H proximity and (13)C-(1)H connectivity. In addition, the 2D (F1/F2) (1)H/(13)C chemical shift correlation spectrum, incorporated with proton magnetization exchange via the fp-RFDR recoupling of (1)H-(1)H dipolar couplings, enables the measurement of proximities between (13)C and even the remote non-carbon-bonded protons. The 3D experiment also gives three-spin proximities of (1)H-(1)H-(13)C chains. Experimental results obtained from powder samples of L-alanine and L-histidine ⋅ H2O ⋅ HCl demonstrate the efficiency of the 3D experiment.

  18. Visualization and Analysis of 3D Gene Expression Data

    SciTech Connect

    Bethel, E. Wes; Rubel, Oliver; Weber, Gunther H.; Hamann, Bernd; Hagen, Hans

    2007-10-25

    Recent methods for extracting precise measurements ofspatial gene expression patterns from three-dimensional (3D) image dataopens the way for new analysis of the complex gene regulatory networkscontrolling animal development. To support analysis of this novel andhighly complex data we developed PointCloudXplore (PCX), an integratedvisualization framework that supports dedicated multi-modal, physical andinformation visualization views along with algorithms to aid in analyzingthe relationships between gene expression levels. Using PCX, we helpedour science stakeholders to address many questions in 3D gene expressionresearch, e.g., to objectively define spatial pattern boundaries andtemporal profiles of genes and to analyze how mRNA patterns arecontrolled by their regulatory transcription factors.

  19. Advanced computational tools for 3-D seismic analysis

    SciTech Connect

    Barhen, J.; Glover, C.W.; Protopopescu, V.A.

    1996-06-01

    The global objective of this effort is to develop advanced computational tools for 3-D seismic analysis, and test the products using a model dataset developed under the joint aegis of the United States` Society of Exploration Geophysicists (SEG) and the European Association of Exploration Geophysicists (EAEG). The goal is to enhance the value to the oil industry of the SEG/EAEG modeling project, carried out with US Department of Energy (DOE) funding in FY` 93-95. The primary objective of the ORNL Center for Engineering Systems Advanced Research (CESAR) is to spearhead the computational innovations techniques that would enable a revolutionary advance in 3-D seismic analysis. The CESAR effort is carried out in collaboration with world-class domain experts from leading universities, and in close coordination with other national laboratories and oil industry partners.

  20. Quantitative Analysis of Autophagy using Advanced 3D Fluorescence Microscopy

    PubMed Central

    Changou, Chun A.; Wolfson, Deanna L.; Ahluwalia, Balpreet Singh; Bold, Richard J.; Kung, Hsing-Jien; Chuang, Frank Y.S.

    2013-01-01

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine1. This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)1,10. Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)1,2,3. Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation4,5. Although the essential components of this pathway are well-characterized6,7,8,9, many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy11,12. Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early stages of

  1. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    PubMed

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-01-01

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  2. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    PubMed

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-05-03

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  3. Structure Segmentation and Transfer Faults in the Marcellus Shale, Clearfield County, Pennsylvania: Implications for Gas Recovery Efficiency and Risk Assessment Using 3D Seismic Attribute Analysis

    NASA Astrophysics Data System (ADS)

    Roberts, Emily D.

    The Marcellus Shale has become an important unconventional gas reservoir in the oil and gas industry. Fractures within this organic-rich black shale serve as an important component of porosity and permeability useful in enhancing production. Horizontal drilling is the primary approach for extracting hydrocarbons in the Marcellus Shale. Typically, wells are drilled perpendicular to natural fractures in an attempt to intersect fractures for effective hydraulic stimulation. If the fractures are contained within the shale, then hydraulic fracturing can enhance permeability by further breaking the already weakened rock. However, natural fractures can affect hydraulic stimulations by absorbing and/or redirecting the energy away from the wellbore, causing a decreased efficiency in gas recovery, as has been the case for the Clearfield County, Pennsylvania study area. Estimating appropriate distances away from faults and fractures, which may limit hydrocarbon recovery, is essential to reducing the risk of injection fluid migration along these faults. In an attempt to mitigate the negative influences of natural fractures on hydrocarbon extraction within the Marcellus Shale, fractures were analyzed through the aid of both traditional and advanced seismic attributes including variance, curvature, ant tracking, and waveform model regression. Through the integration of well log interpretations and seismic data, a detailed assessment of structural discontinuities that may decrease the recovery efficiency of hydrocarbons was conducted. High-quality 3D seismic data in Central Pennsylvania show regional folds and thrusts above the major detachment interval of the Salina Salt. In addition to the regional detachment folds and thrusts, cross-regional, northwest-trending lineaments were mapped. These lineaments may pose a threat to hydrocarbon productivity and recovery efficiency due to faults and fractures acting as paths of least resistance for induced hydraulic stimulation fluids

  4. Molecular cloning, expression pattern, and 3D structural analysis of the MHC class IIB gene in the Chinese longsnout catfish (Leiocassis longirostris).

    PubMed

    Shen, Tong; Xu, Shixia; Yang, Mei; Pang, Shuying; Yang, Guang

    2011-05-15

    stomach, and low or negligible expression in heart. Homology modelling has been applied to create a 3D model of longsnout catfish MHC class IIB, with features evaluated and discussed to investigate its interaction with CD4 participating in antigen recognition. The present findings will provide valuable information for understanding structure, function, expression, and molecular polymorphism of MHC class IIB in adaptive immunity of the Chinese longsnout catfish and teleost. PMID:21377740

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

    PubMed

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

    2012-05-01

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

  6. 3D OCT imaging in clinical settings: toward quantitative measurements of retinal structures

    NASA Astrophysics Data System (ADS)

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

    2006-02-01

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

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

    PubMed Central

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

    2014-01-01

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

  8. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  9. Beam Optics Analysis - An Advanced 3D Trajectory Code

    SciTech Connect

    Ives, R. Lawrence; Bui, Thuc; Vogler, William; Neilson, Jeff; Read, Mike; Shephard, Mark; Bauer, Andrew; Datta, Dibyendu; Beal, Mark

    2006-01-03

    Calabazas Creek Research, Inc. has completed initial development of an advanced, 3D program for modeling electron trajectories in electromagnetic fields. The code is being used to design complex guns and collectors. Beam Optics Analysis (BOA) is a fully relativistic, charged particle code using adaptive, finite element meshing. Geometrical input is imported from CAD programs generating ACIS-formatted files. Parametric data is inputted using an intuitive, graphical user interface (GUI), which also provides control of convergence, accuracy, and post processing. The program includes a magnetic field solver, and magnetic information can be imported from Maxwell 2D/3D and other programs. The program supports thermionic emission and injected beams. Secondary electron emission is also supported, including multiple generations. Work on field emission is in progress as well as implementation of computer optimization of both the geometry and operating parameters. The principle features of the program and its capabilities are presented.

  10. Beam Optics Analysis — An Advanced 3D Trajectory Code

    NASA Astrophysics Data System (ADS)

    Ives, R. Lawrence; Bui, Thuc; Vogler, William; Neilson, Jeff; Read, Mike; Shephard, Mark; Bauer, Andrew; Datta, Dibyendu; Beal, Mark

    2006-01-01

    Calabazas Creek Research, Inc. has completed initial development of an advanced, 3D program for modeling electron trajectories in electromagnetic fields. The code is being used to design complex guns and collectors. Beam Optics Analysis (BOA) is a fully relativistic, charged particle code using adaptive, finite element meshing. Geometrical input is imported from CAD programs generating ACIS-formatted files. Parametric data is inputted using an intuitive, graphical user interface (GUI), which also provides control of convergence, accuracy, and post processing. The program includes a magnetic field solver, and magnetic information can be imported from Maxwell 2D/3D and other programs. The program supports thermionic emission and injected beams. Secondary electron emission is also supported, including multiple generations. Work on field emission is in progress as well as implementation of computer optimization of both the geometry and operating parameters. The principle features of the program and its capabilities are presented.

  11. User's Manual for DuctE3D: A Program for 3D Euler Unsteady Aerodynamic and Aeroelastic Analysis of Ducted Fans

    NASA Technical Reports Server (NTRS)

    Srivastava, R.; Reddy, T. S. R.

    1997-01-01

    The program DuctE3D is used for steady or unsteady aerodynamic and aeroelastic analysis of ducted fans. This guide describes the input data required and the output files generated, in using DuctE3D. The analysis solves three dimensional unsteady, compressible Euler equations to obtain the aerodynamic forces. A normal mode structural analysis is used to obtain the aeroelastic equations, which are solved using either the time domain or the frequency domain solution method. Sample input and output files are included in this guide for steady aerodynamic analysis and aeroelastic analysis of an isolated fan row.

  12. Uncertainty Analysis for RELAP5-3D

    SciTech Connect

    Aaron J. Pawel; Dr. George L. Mesina

    2011-08-01

    In its current state, RELAP5-3D is a 'best-estimate' code; it is one of our most reliable programs for modeling what occurs within reactor systems in transients from given initial conditions. This code, however, remains an estimator. A statistical analysis has been performed that begins to lay the foundation for a full uncertainty analysis. By varying the inputs over assumed probability density functions, the output parameters were shown to vary. Using such statistical tools as means, variances, and tolerance intervals, a picture of how uncertain the results are based on the uncertainty of the inputs has been obtained.

  13. Optical 3D-coordinate measuring system using structured light

    NASA Astrophysics Data System (ADS)

    Schreiber, Wolfgang; Notni, Gunther; Kuehmstedt, Peter; Gerber, Joerg; Kowarschik, Richard M.

    1996-09-01

    The paper is aimed at the description of an optical shape measuring technique based on a consistent principle using fringe projection technique. We demonstrate a real 3D- coordinate measuring system where the sale of coordinates is given only by the illumination-structures. This method has the advantages that the aberration of the observing system and the depth-dependent imaging scale have no influence on the measuring accuracy and, moreover, the measurements are independent of the position of the camera with respect to the object under test. Furthermore, it is shown that the influence of specular effects of the surface on the measuring result can be eliminated. Moreover, we developed a very simple algorithm to calibrate the measuring system. The measuring examples show that a measuring accuracy of 10-4 (i.e. 10 micrometers ) within an object volume of 100 X 100 X 70 mm3 is achievable. Furthermore, it is demonstrated that the set of coordinate values can be processed in CNC- and CAD-systems.

  14. Breast tumor angiogenesis analysis using 3D power Doppler ultrasound

    NASA Astrophysics Data System (ADS)

    Chang, Ruey-Feng; Huang, Sheng-Fang; Lee, Yu-Hau; Chen, Dar-Ren; Moon, Woo Kyung

    2006-03-01

    Angiogenesis is the process that correlates to tumor growth, invasion, and metastasis. Breast cancer angiogenesis has been the most extensively studied and now serves as a paradigm for understanding the biology of angiogenesis and its effects on tumor outcome and patient prognosis. Most studies on characterization of angiogenesis focus on pixel/voxel counts more than morphological analysis. Nevertheless, in cancer, the blood flow is greatly affected by the morphological changes, such as the number of vessels, branching pattern, length, and diameter. This paper presents a computer-aided diagnostic (CAD) system that can quantify vascular morphology using 3-D power Doppler ultrasound (US) on breast tumors. We propose a scheme to extract the morphological information from angiography and to relate them to tumor diagnosis outcome. At first, a 3-D thinning algorithm helps narrow down the vessels into their skeletons. The measurements of vascular morphology significantly rely on the traversing of the vascular trees produced from skeletons. Our study of 3-D assessment of vascular morphological features regards vessel count, length, bifurcation, and diameter of vessels. Investigations into 221 solid breast tumors including 110 benign and 111 malignant cases, the p values using the Student's t-test for all features are less than 0.05 indicating that the proposed features are deemed statistically significant. Our scheme focuses on the vascular architecture without involving the technique of tumor segmentation. The results show that the proposed method is feasible, and have a good agreement with the diagnosis of the pathologists.

  15. USM3D Analysis of Low Boom Configuration

    NASA Technical Reports Server (NTRS)

    Carter, Melissa B.; Campbell, Richard L.; Nayani, Sudheer N.

    2011-01-01

    In the past few years considerable improvement was made in NASA's in house boom prediction capability. As part of this improved capability, the USM3D Navier-Stokes flow solver, when combined with a suitable unstructured grid, went from accurately predicting boom signatures at 1 body length to 10 body lengths. Since that time, the research emphasis has shifted from analysis to the design of supersonic configurations with boom signature mitigation In order to design an aircraft, the techniques for accurately predicting boom and drag need to be determined. This paper compares CFD results with the wind tunnel experimental results conducted on a Gulfstream reduced boom and drag configuration. Two different wind-tunnel models were designed and tested for drag and boom data. The goal of this study was to assess USM3D capability for predicting both boom and drag characteristics. Overall, USM3D coupled with a grid that was sheared and stretched was able to reasonably predict boom signature. The computational drag polar matched the experimental results for a lift coefficient above 0.1 despite some mismatch in the predicted lift-curve slope.

  16. About the automated pattern creation of 3D jacquard double needle bed warp knitted structures

    NASA Astrophysics Data System (ADS)

    Renkens, W.; Kyosev, Y.

    2016-07-01

    Three dimensional structures can be produced on jacquard warp knitting machines with double needle bed. This work presents theoretical considerations about the modelling and simulation of these structures. After that a method is described, how to obtain production parameters from the simulation data. The analysis demonstrates, that the automated pattern creation of 3D structures is not always possible and not all mathematical solutions of the problem can be knittable.

  17. How to Deal with Low-Resolution Target Structures: Using SAR, Ensemble Docking, Hydropathic Analysis, and 3D-QSAR to Definitively Map the αβ-Tubulin Colchicine Site

    PubMed Central

    Da, Chenxiao; Mooberry, Susan L.; Gupton, John T.; Kellogg, Glen E.

    2013-01-01

    αβ-tubulin colchicine site inhibitors (CSIs) from four scaffolds that we previously tested for antiproliferative activity were modeled to better understand their effect on microtubules. Docking models, constructed by exploiting the SAR of a pyrrole subset and HINT scoring, guided ensemble docking of all 59 compounds. This conformation set and two variants having progressively less structure knowledge were subjected to CoMFA, CoMFA+HINT, and CoMSIA 3D-QSAR analyses. The CoMFA+HINT model (docked alignment) showed the best statistics: leave-one-out q2 of 0.616, r2 of 0.949 and r2pred (internal test set) of 0.755. An external (tested in other laboratories) collection of 24 CSIs from eight scaffolds were evaluated with the 3D-QSAR models, which correctly ranked their activity trends in 7/8 scaffolds for CoMFA+HINT (8/8 for CoMFA). The combination of SAR, ensemble docking, hydropathic analysis and 3D-QSAR provides an atomic-scale colchicine site model more consistent with a target structure resolution much higher than the ~3.6 Å available for αβ-tubulin. PMID:23961916

  18. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures

    PubMed Central

    Wang, Jian; Zhao, Yunjie; Zhu, Chunyan; Xiao, Yi

    2015-01-01

    Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models. PMID:25712091

  19. Analysis of the 3D distribution of stacked self-assembled quantum dots by electron tomography

    PubMed Central

    2012-01-01

    The 3D distribution of self-assembled stacked quantum dots (QDs) is a key parameter to obtain the highest performance in a variety of optoelectronic devices. In this work, we have measured this distribution in 3D using a combined procedure of needle-shaped specimen preparation and electron tomography. We show that conventional 2D measurements of the distribution of QDs are not reliable, and only 3D analysis allows an accurate correlation between the growth design and the structural characteristics. PMID:23249477

  20. The feasibility of photo-based 3D modeling for the structures by using a common digital camera

    NASA Astrophysics Data System (ADS)

    Li, Ping; Zhang, Jin-quan; Li, Wan-heng; Lv, Jian-ming; Wang, Xin-zheng

    2011-12-01

    This article explored the method of photo-based 3D modeling for the arc bridge structures by ordinary digital camera. Firstly, a series of processes had been studied by using ordinary digital camera that included the camera calibration, data acquisition, data management, and 3D orientation, setting scale and textures, etc., then the 3D model from photos can be built. The model can be measured, edited and close to the real structures. Take an interior masonry arch bridge as an example, build 3D model through the processes above by using camera HP CB350. The 3D model can be integrated with the loading conditions and material properties, to provide the detailed data for analyzing the structure. This paper has accumulated the experience in data acquisition and modeling methods. The methods can be applied to other structural analysis, and other conditions of 3D modeling with fast and economic advantages.

  1. The development of a 3D risk analysis method.

    PubMed

    I, Yet-Pole; Cheng, Te-Lung

    2008-05-01

    Much attention has been paid to the quantitative risk analysis (QRA) research in recent years due to more and more severe disasters that have happened in the process industries. Owing to its calculation complexity, very few software, such as SAFETI, can really make the risk presentation meet the practice requirements. However, the traditional risk presentation method, like the individual risk contour in SAFETI, is mainly based on the consequence analysis results of dispersion modeling, which usually assumes that the vapor cloud disperses over a constant ground roughness on a flat terrain with no obstructions and concentration fluctuations, which is quite different from the real situations of a chemical process plant. All these models usually over-predict the hazardous regions in order to maintain their conservativeness, which also increases the uncertainty of the simulation results. On the other hand, a more rigorous model such as the computational fluid dynamics (CFD) model can resolve the previous limitations; however, it cannot resolve the complexity of risk calculations. In this research, a conceptual three-dimensional (3D) risk calculation method was proposed via the combination of results of a series of CFD simulations with some post-processing procedures to obtain the 3D individual risk iso-surfaces. It is believed that such technique will not only be limited to risk analysis at ground level, but also be extended into aerial, submarine, or space risk analyses in the near future.

  2. 3D Global Coronal Density Structure and Associated Magnetic Field near Solar Maximum

    NASA Astrophysics Data System (ADS)

    Kramar, Maxim; Airapetian, Vladimir; Lin, Haosheng

    2016-08-01

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

  3. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays.

  4. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGES

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

  5. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    SciTech Connect

    Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

    2015-05-05

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.

  6. RNAssess--a web server for quality assessment of RNA 3D structures.

    PubMed

    Lukasiak, Piotr; Antczak, Maciej; Ratajczak, Tomasz; Szachniuk, Marta; Popenda, Mariusz; Adamiak, Ryszard W; Blazewicz, Jacek

    2015-07-01

    Nowadays, various methodologies can be applied to model RNA 3D structure. Thus, the plausible quality assessment of 3D models has a fundamental impact on the progress of structural bioinformatics. Here, we present RNAssess server, a novel tool dedicated to visual evaluation of RNA 3D models in the context of the known reference structure for a wide range of accuracy levels (from atomic to the whole molecule perspective). The proposed server is based on the concept of local neighborhood, defined as a set of atoms observed within a sphere localized around a central atom of a particular residue. A distinctive feature of our server is the ability to perform simultaneous visual analysis of the model-reference structure coherence. RNAssess supports the quality assessment through delivering both static and interactive visualizations that allows an easy identification of native-like models and/or chosen structural regions of the analyzed molecule. A combination of results provided by RNAssess allows us to rank analyzed models. RNAssess offers new route to a fast and efficient 3D model evaluation suitable for the RNA-Puzzles challenge. The proposed automated tool is implemented as a free and open to all users web server with an user-friendly interface and can be accessed at: http://rnassess.cs.put.poznan.pl/. PMID:26068469

  7. 3D-QSAR and 3D-QSSR studies of thieno[2,3-d]pyrimidin-4-yl hydrazone analogues as CDK4 inhibitors by CoMFA analysis

    PubMed Central

    Cai, Bao-qin; Jin, Hai-xiao; Yan, Xiao-jun; Zhu, Peng; Hu, Gui-xiang

    2014-01-01

    Aim: To investigate the structural basis underlying potency and selectivity of a series of novel analogues of thieno[2,3-d]pyrimidin-4-yl hydrazones as cyclin-dependent kinase 4 (CDK4) inhibitors and to use this information for drug design strategies. Methods: Three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis (CoMFA) were conducted on a training set of 48 compounds. Partial least squares (PLS) analysis was employed. External validation was performed with a test set of 9 compounds. Results: The obtained 3D-QSAR model (q2=0.724, r2=0.965, r2pred=0.945) and 3D-QSSR model (q2=0.742, r2=0.923, r2pred=0.863) were robust and predictive. Contour maps with good compatibility to active binding sites provided insight into the potentially important structural features required to enhance activity and selectivity. The contour maps indicated that bulky groups at R1 position could potentially enhance CDK4 inhibitory activity, whereas bulky groups at R3 position have the opposite effect. Appropriate incorporation of bulky electropositive groups at R4 position is favorable and could improve both potency and selectivity to CDK4. Conclusion: These two models provide useful information to guide drug design strategies aimed at obtaining potent and selective CDK4 inhibitors. PMID:24122012

  8. Uncertainty Analysis of RELAP5-3D

    SciTech Connect

    Alexandra E Gertman; Dr. George L Mesina

    2012-07-01

    As world-wide energy consumption continues to increase, so does the demand for the use of alternative energy sources, such as Nuclear Energy. Nuclear Power Plants currently supply over 370 gigawatts of electricity, and more than 60 new nuclear reactors have been commissioned by 15 different countries. The primary concern for Nuclear Power Plant operation and lisencing has been safety. The safety of the operation of Nuclear Power Plants is no simple matter- it involves the training of operators, design of the reactor, as well as equipment and design upgrades throughout the lifetime of the reactor, etc. To safely design, operate, and understand nuclear power plants, industry and government alike have relied upon the use of best-estimate simulation codes, which allow for an accurate model of any given plant to be created with well-defined margins of safety. The most widely used of these best-estimate simulation codes in the Nuclear Power industry is RELAP5-3D. Our project focused on improving the modeling capabilities of RELAP5-3D by developing uncertainty estimates for its calculations. This work involved analyzing high, medium, and low ranked phenomena from an INL PIRT on a small break Loss-Of-Coolant Accident as wall as an analysis of a large break Loss-Of- Coolant Accident. Statistical analyses were performed using correlation coefficients. To perform the studies, computer programs were written that modify a template RELAP5 input deck to produce one deck for each combination of key input parameters. Python scripting enabled the running of the generated input files with RELAP5-3D on INL’s massively parallel cluster system. Data from the studies was collected and analyzed with SAS. A summary of the results of our studies are presented.

  9. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

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

  10. Postprocessing techniques for 3D non-linear structures

    NASA Technical Reports Server (NTRS)

    Gallagher, Richard S.

    1987-01-01

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

  11. Investigation of the deep crustal structure and magmatic activity at the NW Hellenic Volcanic Arc with 3-D aeromagnetic inversion and seimotectonic analysis.

    NASA Astrophysics Data System (ADS)

    Efstathiou, Angeliki; Tzanis, Andreas; Chailas, Stylianos; Stamatakis, Michael

    2013-04-01

    We report the results of a joint analysis of geophysical (aeromagnetic) and seismotectonic data, applied to the investigation of the deep structure, magmatic activity and geothermal potential of the north-western stretches of the Hellenic Volcanic Arc (HVA). The HVA is usually considered to be a single arcuate entity stretching from Sousaki (near Corinth) at the NW, to Nisyros Island at the SE. However, different types of and their ages indicate the presence of two different volcanic groups. Our study focuses on the northern part of the west (older) volcanic group and includes the Crommyonian (Sousaki) volcanic field at the west end of Megaris peninsula (east margin on the contemporary Corinth Rift), the Aegina and Methana volcanic complex at the Saronic Gulf, where typical Quaternary calc-alkaline volcanics predominate, and the Argolid peninsula to the south and south-west. In addition to the rocks associated with Quaternary volcanism, the study area includes a series of Mesozoic ultramafic (ophiolitic) outcrops at the Megaris peninsula, to the north and north-east of the Crommyonian volcanic field, as well as throughout the Argolid. A major deep structural and tectonic feature of the study area, and one with profound influence on crustal deformation and the evolution of rapidly deforming extensional structures like the Corinth Rift and the Saronic Gulf, is the local geometry and dynamics of the African oceanic crust subducting beneath the Aegean plate. Locally, the subducting slab has a NNW strike and ENE plunge, with the dip angle changing rapidly (steepening) approx. beneath the Argolid. The aeromagnetic data was extracted from the recently (re)compiled aeromagnetic map of Greece (Chailas et al, 2010) and was inverted with the UBC-GIF magnetic inversion suite (Li and Oldenburg, 1996). The inversion included rigorous geological constraints introduced by means of numerous in-situ magnetic susceptibility measurements. The inversion has imaged several isolated

  12. Dynamical Systems Analysis of Fully 3D Ocean Features

    NASA Astrophysics Data System (ADS)

    Pratt, L. J.

    2011-12-01

    Dynamical systems analysis of transport and stirring processes has been developed most thoroughly for 2D flow fields. The calculation of manifolds, turnstile lobes, transport barriers, etc. based on observations of the ocean is most often conducted near the sea surface, whereas analyses at depth, usually carried out with model output, is normally confined to constant-z surfaces. At the meoscale and larger, ocean flows are quasi 2D, but smaller scale (submesoscale) motions, including mixed layer phenomena with significant vertical velocity, may be predominantly 3D. The zoology of hyperbolic trajectories becomes richer in such cases and their attendant manifolds are much more difficult to calculate. I will describe some of the basic geometrical features and corresponding Lagrangian Coherent Features expected to arise in upper ocean fronts, eddies, and Langmuir circulations. Traditional GFD models such as the rotating can flow may capture the important generic features. The dynamical systems approach is most helpful when these features are coherent and persistent and the implications and difficulties for this requirement in fully 3D flows will also be discussed.

  13. 3D-Geomorphometrics tooth shape analysis in hypodontia

    PubMed Central

    Al-Shahrani, Ibrahim; Dirks, Wendy; Jepson, Nicholas; Khalaf, Khaled

    2014-01-01

    Assessment of tooth morphology is an important part of the diagnosis and management of hypodontia patients. Several techniques have been used to analyze tooth form in hypodontia patients and these have shown smaller tooth dimensions and anomalous tooth shapes in patients with hypodontia when compared with controls. However, previous studies have mainly used 2D images and provided limited information. In the present study, 3D surface-imaging and statistical shape analysis were used to evaluate tooth form differences between hypodontia and control patients. Eighteen anatomical landmarks were recorded on the clinical crown of the lower left first permanent molar of 3D scanned study models of hypodontia and control subjects. The study sample group comprised of 120 hypodontia patients (40 mild, 40 moderate, and 40 severe hypodontia patients) and 40 age- and sex-matched controls. Procrustes coordinates were utilized to scale and superimpose the landmark coordinate data and then were subjected to principal component analysis (PCA). Subsequently, differences in shape as well as size were tested statistically using allometric analysis and MANOVA. Significant interaction was found between the two factor variables “group” and “sex” (p < 0.002). Overall expected accuracies were 66 and 56% for females and males, respectively, in the cross-validated discriminant-analysis using the first 20 PCs. Hypodontia groups showed significant shape differences compared with the control subjects (p < 0.0001). Significant differences in tooth crown shape were also found between sexes (p < 0.0001) within groups. Furthermore, the degree of variation in tooth form was proportional to the degree of the severity of the hypodontia. Thus, quantitative measurement of tooth shape in hypodontia patients may enhance the multidisciplinary management of those patients. PMID:24795649

  14. Comparative visual analysis of 3D urban wind simulations

    NASA Astrophysics Data System (ADS)

    Röber, Niklas; Salim, Mohamed; Grawe, David; Leitl, Bernd; Böttinger, Michael; Schlünzen, Heinke

    2016-04-01

    Climate simulations are conducted in large quantity for a variety of different applications. Many of these simulations focus on global developments and study the Earth's climate system using a coupled atmosphere ocean model. Other simulations are performed on much smaller regional scales, to study very small fine grained climatic effects. These microscale climate simulations pose similar, yet also different, challenges for the visualization and the analysis of the simulation data. Modern interactive visualization and data analysis techniques are very powerful tools to assist the researcher in answering and communicating complex research questions. This presentation discusses comparative visualization for several different wind simulations, which were created using the microscale climate model MITRAS. The simulations differ in wind direction and speed, but are all centered on the same simulation domain: An area of Hamburg-Wilhelmsburg that hosted the IGA/IBA exhibition in 2013. The experiments contain a scenario case to analyze the effects of single buildings, as well as examine the impact of the Coriolis force within the simulation. The scenario case is additionally compared with real measurements from a wind tunnel experiment to ascertain the accuracy of the simulation and the model itself. We also compare different approaches for tree modeling and evaluate the stability of the model. In this presentation, we describe not only our workflow to efficiently and effectively visualize microscale climate simulation data using common 3D visualization and data analysis techniques, but also discuss how to compare variations of a simulation and how to highlight the subtle differences in between them. For the visualizations we use a range of different 3D tools that feature techniques for statistical data analysis, data selection, as well as linking and brushing.

  15. Identifying Key Structural Features and Spatial Relationships in Archean Microbialites Using 2D and 3D Visualization Methods

    NASA Astrophysics Data System (ADS)

    Stevens, E. W.; Sumner, D. Y.

    2009-12-01

    Microbialites in the 2521 ± 3 Ma Gamohaan Formation, South Africa, have several different end-member morphologies which show distinct growth structures and spatial relationships. We characterized several growth structures and spatial relationships in two samples (DK20 and 2_06) using a combination of 2D and 3D analytical techniques. There are two main goals in studying complicated microbialites with a combination of 2D and 3D methods. First, one can better understand microbialite growth by identifying important structures and structural relationships. Once structures are identified, the order in which the structures formed and how they are related can be inferred from observations of crosscutting relationships. Second, it is important to use both 2D and 3D methods to correlate 3D observations with those in 2D that are more common in the field. Combining analysis provides significantly more insight into the 3D morphology of microbial structures. In our studies, 2D analysis consisted of describing polished slabs and serial sections created by grinding down the rock 100 microns at a time. 3D analysis was performed on serial sections visualized in 3D using Vrui and 3DVisualizer software developed at KeckCAVES, UCD (http://keckcaves.org). Data were visualized on a laptop and in an immersive cave system. Both samples contain microbial laminae and more vertically orients microbial "walls" called supports. The relationships between these features created voids now filled with herringbone and blocky calcite crystals. DK20, a classic plumose structure, contains two types of support structures. Both are 1st order structures (1st order structures with organic inclusions and 1st without organic inclusions) interpreted as planar features based on 2D analysis. In the 2D analysis the 1st order structures show v branching relationships as well as single cuspate relationships (two 1st order structures with inclusions merging upward), and single tented relationships (three supports

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

    NASA Astrophysics Data System (ADS)

    Gheorghe, Radu; Tchouprakov, Andrei; Sokolov, Roman

    2013-02-01

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

  17. A lightweight tangible 3D interface for interactive visualization of thin fiber structures.

    PubMed

    Jackson, Bret; Lau, Tung Yuen; Schroeder, David; Toussaint, Kimani C; Keefe, Daniel F

    2013-12-01

    We present a prop-based, tangible interface for 3D interactive visualization of thin fiber structures. These data are commonly found in current bioimaging datasets, for example second-harmonic generation microscopy of collagen fibers in tissue. Our approach uses commodity visualization technologies such as a depth sensing camera and low-cost 3D display. Unlike most current uses of these emerging technologies in the games and graphics communities, we employ the depth sensing camera to create a fish-tank stereoscopic virtual reality system at the scientist's desk that supports tracking of small-scale gestures with objects already found in the work space. We apply the new interface to the problem of interactive exploratory visualization of three-dimensional thin fiber data. A critical task for the visual analysis of these data is understanding patterns in fiber orientation throughout a volume.The interface enables a new, fluid style of data exploration and fiber orientation analysis by using props to provide needed passive-haptic feedback, making 3D interactions with these fiber structures more controlled. We also contribute a low-level algorithm for extracting fiber centerlines from volumetric imaging. The system was designed and evaluated with two biophotonic experts who currently use it in their lab. As compared to typical practice within their field, the new visualization system provides a more effective way to examine and understand the 3D bioimaging datasets they collect.

  18. Colossal Tooling Design: 3D Simulation for Ergonomic Analysis

    NASA Technical Reports Server (NTRS)

    Hunter, Steve L.; Dischinger, Charles; Thomas, Robert E.; Babai, Majid

    2003-01-01

    The application of high-level 3D simulation software to the design phase of colossal mandrel tooling for composite aerospace fuel tanks was accomplished to discover and resolve safety and human engineering problems. The analyses were conducted to determine safety, ergonomic and human engineering aspects of the disassembly process of the fuel tank composite shell mandrel. Three-dimensional graphics high-level software, incorporating various ergonomic analysis algorithms, was utilized to determine if the process was within safety and health boundaries for the workers carrying out these tasks. In addition, the graphical software was extremely helpful in the identification of material handling equipment and devices for the mandrel tooling assembly/disassembly process.

  19. 3D finite element analysis of porous Ti-based alloy prostheses.

    PubMed

    Mircheski, Ile; Gradišar, Marko

    2016-11-01

    In this paper, novel designs of porous acetabular cups are created and tested with 3D finite element analysis (FEA). The aim is to develop a porous acetabular cup with low effective radial stiffness of the structure, which will be near to the architectural and mechanical behavior of the natural bone. For the realization of this research, a 3D-scanner technology was used for obtaining a 3D-CAD model of the pelvis bone, a 3D-CAD software for creating a porous acetabular cup, and a 3D-FEA software for virtual testing of a novel design of the porous acetabular cup. The results obtained from this research reveal that a porous acetabular cup from Ti-based alloys with 60 ± 5% porosity has the mechanical behavior and effective radial stiffness (Young's modulus in radial direction) that meet and exceed the required properties of the natural bone. The virtual testing with 3D-FEA of a novel design with porous structure during the very early stage of the design and the development of orthopedic implants, enables obtaining a new or improved biomedical implant for a relatively short time and reduced price.

  20. Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action.

    PubMed

    Yang, Xianhai; Liu, Huihui; Liu, Jining; Li, Fei; Li, Xuehua; Shi, Lili; Chen, Jingwen

    2016-09-19

    Molecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally-determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure determined process and resolution. PMID:27556396

  1. 3D structuring of biocompatible and biodegradable polymers via stereolithography.

    PubMed

    Gill, Andrew A; Claeyssens, Frederik

    2011-01-01

    The production of user-defined 3D microstructures from biocompatible and biodegradable materials via free-form fabrication is an important step to create off-the-shelf technologies to be used as tissue engineering scaffolds. One method of achieving this is the microstereolithography of block copolymers, allowing high resolution microstructuring of materials with tuneable physical properties. A versatile protocol for the production and photofunctionalisation of pre-polymers for microstereolithography is presented along with a discussion of the possible microstereolithography set-ups and previous work in the field.

  2. Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

    NASA Astrophysics Data System (ADS)

    Strait, E. J.; King, J. D.; Hanson, J. M.; Logan, N. C.

    2016-11-01

    An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ˜10-3 to 10-5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

  3. Analytical 3-D p-element for quadrilateral plates—Part 1: Thick isotropic plate structures

    NASA Astrophysics Data System (ADS)

    Zhu, B.; Leung, A. Y. T.; Li, Q. S.; Lu, J. W. Z.; Zhang, X. C.

    2007-06-01

    An analytical three-dimensional (3-D) p-version element for the vibration analysis of arbitrary quadrilateral thick plates is presented. With the additional hierarchical shape functions and analytically integrated element matrices, the computed accuracy is considerably improved. The computed natural frequencies of cantilever and simply supported square plates show that the convergence rate of the present element is very fast with respect to the number of hierarchical terms and it can predict very accurate modes. The element is applicable to the free vibration analysis of quadrilateral, polygonal plates as well as 3-D space structures. The continuous wavelet transform (CWT) is applied for the identification of damping ratios. Based on the Rayleigh damping model, the damped vibration response is obtained. A simple experiment is performed to verify the predicted vibration responses. The results show that the proposed element is also efficient for the vibration response analysis of plates.

  4. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures.

    PubMed

    White, Diana; Coombe, Dennis; Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  5. Building a 3D Virtual Liver: Methods for Simulating Blood Flow and Hepatic Clearance on 3D Structures

    PubMed Central

    Rezania, Vahid; Tuszynski, Jack

    2016-01-01

    In this paper, we develop a spatio-temporal modeling approach to describe blood and drug flow, as well as drug uptake and elimination, on an approximation of the liver. Extending on previously developed computational approaches, we generate an approximation of a liver, which consists of a portal and hepatic vein vasculature structure, embedded in the surrounding liver tissue. The vasculature is generated via constrained constructive optimization, and then converted to a spatial grid of a selected grid size. Estimates for surrounding upscaled lobule tissue properties are then presented appropriate to the same grid size. Simulation of fluid flow and drug metabolism (hepatic clearance) are completed using discretized forms of the relevant convective-diffusive-reactive partial differential equations for these processes. This results in a single stage, uniformly consistent method to simulate equations for blood and drug flow, as well as drug metabolism, on a 3D structure representative of a liver. PMID:27649537

  6. Analysis and dynamic 3D visualization of cerebral blood flow combining 3D and 4D MR image sequences

    NASA Astrophysics Data System (ADS)

    Forkert, Nils Daniel; Säring, Dennis; Fiehler, Jens; Illies, Till; Möller, Dietmar; Handels, Heinz

    2009-02-01

    In this paper we present a method for the dynamic visualization of cerebral blood flow. Spatio-temporal 4D magnetic resonance angiography (MRA) image datasets and 3D MRA datasets with high spatial resolution were acquired for the analysis of arteriovenous malformations (AVMs). One of the main tasks is the combination of the information of the 3D and 4D MRA image sequences. Initially, in the 3D MRA dataset the vessel system is segmented and a 3D surface model is generated. Then, temporal intensity curves are analyzed voxelwise in the 4D MRA image sequences. A curve fitting of the temporal intensity curves to a patient individual reference curve is used to extract the bolus arrival times in the 4D MRA sequences. After non-linear registration of both MRA datasets the extracted hemodynamic information is transferred to the surface model where the time points of inflow can be visualized color coded dynamically over time. The dynamic visualizations computed using the curve fitting method for the estimation of the bolus arrival times were rated superior compared to those computed using conventional approaches for bolus arrival time estimation. In summary the procedure suggested allows a dynamic visualization of the individual hemodynamic situation and better understanding during the visual evaluation of cerebral vascular diseases.

  7. 3D Analysis of HCMV Induced-Nuclear Membrane Structures by FIB/SEM Tomography: Insight into an Unprecedented Membrane Morphology.

    PubMed

    Villinger, Clarissa; Neusser, Gregor; Kranz, Christine; Walther, Paul; Mertens, Thomas

    2015-11-01

    We show that focused ion beam/scanning electron microscopy (FIB/SEM) tomography is an excellent method to analyze the three-dimensional structure of a fibroblast nucleus infected with human cytomegalovirus (HCMV). We found that the previously described infoldings of the inner nuclear membrane, which are unique among its kind, form an extremely complex network of membrane structures not predictable by previous two-dimensional studies. In all cases they contained further invaginations (2nd and 3rd order infoldings). Quantification revealed 5498HCMV capsids within two nuclear segments, allowing an estimate of 15,000 to 30,000 capsids in the entire nucleus five days post infection. Only 0.8% proved to be enveloped capsids which were exclusively detected in 1st order infoldings (perinuclear space). Distribution of the capsids between 1st, 2nd and 3rd order infoldings is in complete agreement with the envelopment/de-envelopment model for egress of HCMV capsids from the nucleus and we confirm that capsid budding does occur at the large infoldings. Based on our results we propose the pushing membrane model: HCMV infection induces local disruption of the nuclear lamina and synthesis of new membrane material which is pushed into the nucleoplasm, forming complex membrane infoldings in a highly abundant manner, which then may be also used by nucleocapsids for budding. PMID:26556360

  8. 3D Analysis of HCMV Induced-Nuclear Membrane Structures by FIB/SEM Tomography: Insight into an Unprecedented Membrane Morphology

    PubMed Central

    Villinger, Clarissa; Neusser, Gregor; Kranz, Christine; Walther, Paul; Mertens, Thomas

    2015-01-01

    We show that focused ion beam/scanning electron microscopy (FIB/SEM) tomography is an excellent method to analyze the three-dimensional structure of a fibroblast nucleus infected with human cytomegalovirus (HCMV). We found that the previously described infoldings of the inner nuclear membrane, which are unique among its kind, form an extremely complex network of membrane structures not predictable by previous two-dimensional studies. In all cases they contained further invaginations (2nd and 3rd order infoldings). Quantification revealed 5498 HCMV capsids within two nuclear segments, allowing an estimate of 15,000 to 30,000 capsids in the entire nucleus five days post infection. Only 0.8% proved to be enveloped capsids which were exclusively detected in 1st order infoldings (perinuclear space). Distribution of the capsids between 1st, 2nd and 3rd order infoldings is in complete agreement with the envelopment/de-envelopment model for egress of HCMV capsids from the nucleus and we confirm that capsid budding does occur at the large infoldings. Based on our results we propose the pushing membrane model: HCMV infection induces local disruption of the nuclear lamina and synthesis of new membrane material which is pushed into the nucleoplasm, forming complex membrane infoldings in a highly abundant manner, which then may be also used by nucleocapsids for budding. PMID:26556360

  9. 3D Finite Element Analysis of Particle-Reinforced Aluminum

    NASA Technical Reports Server (NTRS)

    Shen, H.; Lissenden, C. J.

    2002-01-01

    Deformation in particle-reinforced aluminum has been simulated using three distinct types of finite element model: a three-dimensional repeating unit cell, a three-dimensional multi-particle model, and two-dimensional multi-particle models. The repeating unit cell model represents a fictitious periodic cubic array of particles. The 3D multi-particle (3D-MP) model represents randomly placed and oriented particles. The 2D generalized plane strain multi-particle models were obtained from planar sections through the 3D-MP model. These models were used to study the tensile macroscopic stress-strain response and the associated stress and strain distributions in an elastoplastic matrix. The results indicate that the 2D model having a particle area fraction equal to the particle representative volume fraction of the 3D models predicted the same macroscopic stress-strain response as the 3D models. However, there are fluctuations in the particle area fraction in a representative volume element. As expected, predictions from 2D models having different particle area fractions do not agree with predictions from 3D models. More importantly, it was found that the microscopic stress and strain distributions from the 2D models do not agree with those from the 3D-MP model. Specifically, the plastic strain distribution predicted by the 2D model is banded along lines inclined at 45 deg from the loading axis while the 3D model prediction is not. Additionally, the triaxial stress and maximum principal stress distributions predicted by 2D and 3D models do not agree. Thus, it appears necessary to use a multi-particle 3D model to accurately predict material responses that depend on local effects, such as strain-to-failure, fracture toughness, and fatigue life.

  10. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  11. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

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

  12. 3D Printing: 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles (Adv. Mater. 19/2016).

    PubMed

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

    2016-05-01

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

  13. The first 3-D LaIII-SrII heterometallic complex: Synthesis, structure and luminescent properties

    NASA Astrophysics Data System (ADS)

    Hong, Zhiwei; Ran, Jingwen; Li, Tao; Chen, Yanmei

    2016-10-01

    The first 3-D LaIII-SrII heterometallic complex, namely [La2Sr(pda)4(H2O)4]n·6nH2O (1, H2pda = pyridine-2,6-dicarboxylic acid), has been successfully synthesized under solvothermal conditions. Single crystal X-ray diffraction analysis reveals that complex 1 features a 3-D porous framework and displays a new topology. The crystal structure can be simplified to a 4,6-connected 3-D network with Schläfli symbol of {34·42·88·9}2{34·42}. The crystals also have been characterized by X-ray powder diffraction, elemental analysis, thermal analysis, and IR spectroscopy. The infrared spectral analysis indicates that complex 1 is a carboxylate coordinated compound, several water molecules exist in the compound. The thermal study shows that there are ten water molecules in the crystal structure. The luminescent property has also been investigated. It shows a blue-purple fluorescence emission.

  14. 3D form line construction by structural field interpolation (SFI) of geologic strike and dip observations

    NASA Astrophysics Data System (ADS)

    Hillier, Michael; de Kemp, Eric; Schetselaar, Ernst

    2013-06-01

    Interpreting and modelling geometries of complex geologic structures from strike/dip measurements using manually-drafted structural form lines is labour intensive, irreproducible and inherently limited to two dimensions. Herein, the structural field interpolation (SFI) algorithm is presented that overcomes these limitations by constructing 3D structural form lines from the vector components of strike/dip measurements. The SFI interpolation algorithm employs an anisotropic inverse distance weighting scheme derived from eigen analysis of the poles to strike/dip measurements within a neighbourhood of user defined dimension and shape (ellipsoidal to spherical) and honours younging directions, when available. The eigen analysis also provides local estimates of the plunge vector and associated Woodcock distribution properties to assure plunge-normal structural form line reconstruction with unidirectional propagation of form lines across fold and fan structures. The method is advantageous for modelling geometries of geologic structures from a wide range of structurally anisotropic data. Modelled vector fields from three case studies are presented that reproduce the expected bedding-foliation geometry and provide reasonable representation of complex folds from local to regional scales. Results illustrate the potential for using vector fields to support geologic interpretation through the direct visualization of geometric trends of structural features in 3D.

  15. Aeroelastic Analysis of SUGAR Truss-Braced Wing Wind-Tunnel Model Using FUN3D and a Nonlinear Structural Model

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.; Scott, Robert C.; Allen, Timothy J.; Sexton, Bradley W.

    2015-01-01

    Considerable attention has been given in recent years to the design of highly flexible aircraft. The results of numerous studies demonstrate the significant performance benefits of strut-braced wing (SBW) and trussbraced wing (TBW) configurations. Critical aspects of the TBW configuration are its larger aspect ratio, wing span and thinner wings. These aspects increase the importance of considering fluid/structure and control system coupling. This paper presents high-fidelity Navier-Stokes simulations of the dynamic response of the flexible Boeing Subsonic Ultra Green Aircraft Research (SUGAR) truss-braced wing wind-tunnel model. The latest version of the SUGAR TBW finite element model (FEM), v.20, is used in the present simulations. Limit cycle oscillations (LCOs) of the TBW wing/strut/nacelle are simulated at angle-of-attack (AoA) values of -1, 0 and +1 degree. The modal data derived from nonlinear static aeroelastic MSC.Nastran solutions are used at AoAs of -1 and +1 degrees. The LCO amplitude is observed to be dependent on AoA. LCO amplitudes at -1 degree are larger than those at +1 degree. The LCO amplitude at zero degrees is larger than either -1 or +1 degrees. These results correlate well with both wind-tunnel data and the behavior observed in previous studies using linear aerodynamics. The LCO onset at zero degrees AoA has also been computed using unloaded v.20 FEM modes. While the v.20 model increases the dynamic pressure at which LCO onset is observed, it is found that the LCO onset at and above Mach 0.82 is much different than that produced by an earlier version of the FEM, v. 19.

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

    NASA Technical Reports Server (NTRS)

    Riggs, H. R.

    2000-01-01

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

  17. The three-dimensional elemental distribution based on the surface topography by confocal 3D-XRF analysis

    NASA Astrophysics Data System (ADS)

    Yi, Longtao; Qin, Min; Wang, Kai; Lin, Xue; Peng, Shiqi; Sun, Tianxi; Liu, Zhiguo

    2016-09-01

    Confocal three-dimensional micro-X-ray fluorescence (3D-XRF) is a good surface analysis technology widely used to analyse elements and elemental distributions. However, it has rarely been applied to analyse surface topography and 3D elemental mapping in surface morphology. In this study, a surface adaptive algorithm using the progressive approximation method was designed to obtain surface topography. A series of 3D elemental mapping analyses in surface morphology were performed in laboratories to analyse painted pottery fragments from the Majiayao Culture (3300-2900 BC). To the best of our knowledge, for the first time, sample surface topography and 3D elemental mapping were simultaneously obtained. Besides, component and depth analyses were also performed using synchrotron radiation confocal 3D-XRF and tabletop confocal 3D-XRF, respectively. The depth profiles showed that the sample has a layered structure. The 3D elemental mapping showed that the red pigment, black pigment, and pottery coat contain a large amount of Fe, Mn, and Ca, respectively. From the 3D elemental mapping analyses at different depths, a 3D rendering was obtained, clearly showing the 3D distributions of the red pigment, black pigment, and pottery coat. Compared with conventional 3D scanning, this method is time-efficient for analysing 3D elemental distributions and hence especially suitable for samples with non-flat surfaces.

  18. The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.

    PubMed

    Girdlestone, Christopher; Hayward, Steven

    2016-01-01

    DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization. PMID:26540459

  19. Simultaneous Aerodynamic and Structural Design Optimization (SASDO) for a 3-D Wing

    NASA Technical Reports Server (NTRS)

    Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.

    2001-01-01

    The formulation and implementation of an optimization method called Simultaneous Aerodynamic and Structural Design Optimization (SASDO) is shown as an extension of the Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) method. It is extended by the inclusion of structure element sizing parameters as design variables and Finite Element Method (FEM) analysis responses as constraints. The method aims to reduce the computational expense. incurred in performing shape and sizing optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, FEM structural analysis and sensitivity analysis tools. SASDO is applied to a simple. isolated, 3-D wing in inviscid flow. Results show that the method finds the saine local optimum as a conventional optimization method with some reduction in the computational cost and without significant modifications; to the analysis tools.

  20. Understanding Crystal Populations; Looking Towards 3D Quantitative Analysis

    NASA Astrophysics Data System (ADS)

    Jerram, D. A.; Morgan, D. J.

    2010-12-01

    In order to understand volcanic systems, the potential record held within crystal populations needs to be revealed. It is becoming increasingly clear, however, that the crystal populations that arrive at the surface in volcanic eruptions are commonly mixtures of crystals, which may be representative of simple crystallization, recycling of crystals and incorporation of alien crystals. If we can quantify the true 3D population within a sample then we will be able to separate crystals with different histories and begin to interrogate the true and complex plumbing within the volcanic system. Modeling crystal populations is one area where we can investigate the best methodologies to use when dealing with sections through 3D populations. By producing known 3D shapes and sizes with virtual textures and looking at the statistics of shape and size when such populations are sectioned, we are able to gain confidence about what our 2D information is telling us about the population. We can also use this approach to test the size of population we need to analyze. 3D imaging through serial sectioning or x-ray CT, provides a complete 3D quantification of a rocks texture. Individual phases can be identified and in principle the true 3D statistics of the population can be interrogated. In practice we need to develop strategies (as with 2D-3D transformations), that enable a true characterization of the 3D data, and an understanding of the errors and pitfalls that exist. Ultimately, the reproduction of true 3D textures and the wealth of information they hold, is now within our reach.

  1. Multi Length Scale Imaging of Flocculated Estuarine Sediments; Insights into their Complex 3D Structure

    NASA Astrophysics Data System (ADS)

    Wheatland, Jonathan; Bushby, Andy; Droppo, Ian; Carr, Simon; Spencer, Kate

    2015-04-01

    Suspended estuarine sediments form flocs that are compositionally complex, fragile and irregularly shaped. The fate and transport of suspended particulate matter (SPM) is determined by the size, shape, density, porosity and stability of these flocs and prediction of SPM transport requires accurate measurements of these three-dimensional (3D) physical properties. However, the multi-scaled nature of flocs in addition to their fragility makes their characterisation in 3D problematic. Correlative microscopy is a strategy involving the spatial registration of information collected at different scales using several imaging modalities. Previously, conventional optical microscopy (COM) and transmission electron microscopy (TEM) have enabled 2-dimensional (2D) floc characterisation at the gross (> 1 µm) and sub-micron scales respectively. Whilst this has proven insightful there remains a critical spatial and dimensional gap preventing the accurate measurement of geometric properties and an understanding of how structures at different scales are related. Within life sciences volumetric imaging techniques such as 3D micro-computed tomography (3D µCT) and focused ion beam scanning electron microscopy [FIB-SEM (or FIB-tomography)] have been combined to characterise materials at the centimetre to micron scale. Combining these techniques with TEM enables an advanced correlative study, allowing material properties across multiple spatial and dimensional scales to be visualised. The aims of this study are; 1) to formulate an advanced correlative imaging strategy combining 3D µCT, FIB-tomography and TEM; 2) to acquire 3D datasets; 3) to produce a model allowing their co-visualisation; 4) to interpret 3D floc structure. To reduce the chance of structural alterations during analysis samples were first 'fixed' in 2.5% glutaraldehyde/2% formaldehyde before being embedding in Durcupan resin. Intermediate steps were implemented to improve contrast and remove pore water, achieved by the

  2. Crashworthiness analysis using advanced material models in DYNA3D

    SciTech Connect

    Logan, R.W.; Burger, M.J.; McMichael, L.D.; Parkinson, R.D.

    1993-10-22

    As part of an electric vehicle consortium, LLNL and Kaiser Aluminum are conducting experimental and numerical studies on crashworthy aluminum spaceframe designs. They have jointly explored the effect of heat treat on crush behavior and duplicated the experimental behavior with finite-element simulations. The major technical contributions to the state of the art in numerical simulation arise from the development and use of advanced material model descriptions for LLNL`s DYNA3D code. Constitutive model enhancements in both flow and failure have been employed for conventional materials such as low-carbon steels, and also for lighter weight materials such as aluminum and fiber composites being considered for future vehicles. The constitutive model enhancements are developed as extensions from LLNL`s work in anisotropic flow and multiaxial failure modeling. Analysis quality as a function of level of simplification of material behavior and mesh is explored, as well as the penalty in computation cost that must be paid for using more complex models and meshes. The lightweight material modeling technology is being used at the vehicle component level to explore the safety implications of small neighborhood electric vehicles manufactured almost exclusively from these materials.

  3. Multiple 3D RNA Structure Superposition Using Neighbor Joining.

    PubMed

    Hoksza, David; Svozil, Daniel

    2015-01-01

    Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER-a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.

  4. 3-D Printed Ultem 9085 Testing and Analysis

    NASA Technical Reports Server (NTRS)

    Aguilar, Daniel; Christensen, Sean; Fox, Emmet J.

    2015-01-01

    The purpose of this document is to analyze the mechanical properties of 3-D printed Ultem 9085. This document will focus on the capabilities, limitations, and complexities of 3D printing in general, and explain the methods by which this material is tested. Because 3-D printing is a relatively new process that offers an innovative means to produce hardware, it is important that the aerospace community understands its current advantages and limitations, so that future endeavors involving 3-D printing may be completely safe. This document encompasses three main sections: a Slosh damage assessment, a destructive test of 3-D printed Ultem 9085 samples, and a test to verify simulation for the 3-D printed SDP (SPHERES Docking Port). Described below, 'Slosh' and 'SDP' refer to two experiments that are built using Ultem 9085 for use with the SPHERES (Synchronized Position Hold, Engage, Reorient, Experimental Satellites) program onboard the International Space Station (ISS) [16]. The SPHERES Facility is managed out of the National Aeronautics and Space Administration (NASA) Ames Research Center in California.

  5. A procedure to average 3D anatomical structures.

    PubMed

    Subramanya, K; Dean, D

    2000-12-01

    Creating a feature-preserving average of three dimensional anatomical surfaces extracted from volume image data is a complex task. Unlike individual images, averages present right-left symmetry and smooth surfaces which give insight into typical proportions. Averaging multiple biological surface images requires careful superimposition and sampling of homologous regions. Our approach to biological surface image averaging grows out of a wireframe surface tessellation approach by Cutting et al. (1993). The surface delineating wires represent high curvature crestlines. By adding tile boundaries in flatter areas the 3D image surface is parametrized into anatomically labeled (homology mapped) grids. We extend the Cutting et al. wireframe approach by encoding the entire surface as a series of B-spline space curves. The crestline averaging algorithm developed by Cutting et al. may then be used for the entire surface. Shape preserving averaging of multiple surfaces requires careful positioning of homologous surface regions such as these B-spline space curves. We test the precision of this new procedure and its ability to appropriately position groups of surfaces in order to produce a shape-preserving average. Our result provides an average that well represents the source images and may be useful clinically as a deformable model or for animation.

  6. Air-structured optical fiber drawn from a 3D-printed preform.

    PubMed

    Cook, Kevin; Canning, John; Leon-Saval, Sergio; Reid, Zane; Hossain, Md Arafat; Comatti, Jade-Edouard; Luo, Yanhua; Peng, Gang-Ding

    2015-09-01

    A structured optical fiber is drawn from a 3D-printed structured preform. Preforms containing a single ring of holes around the core are fabricated using filament made from a modified butadiene polymer. More broadly, 3D printers capable of processing soft glasses, silica, and other materials are likely to come on line in the not-so-distant future. 3D printing of optical preforms signals a new milestone in optical fiber manufacture.

  7. 3D Printing of Conductive Complex Structures with In Situ Generation of Silver Nanoparticles.

    PubMed

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

    2016-05-01

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

  8. 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

  9. 3D texture analysis for classification of second harmonic generation images of human ovarian cancer

    PubMed Central

    Wen, Bruce; Campbell, Kirby R.; Tilbury, Karissa; Nadiarnykh, Oleg; Brewer, Molly A.; Patankar, Manish; Singh, Vikas; Eliceiri, Kevin. W.; Campagnola, Paul J.

    2016-01-01

    Remodeling of the collagen architecture in the extracellular matrix (ECM) has been implicated in ovarian cancer. To quantify these alterations we implemented a form of 3D texture analysis to delineate the fibrillar morphology observed in 3D Second Harmonic Generation (SHG) microscopy image data of normal (1) and high risk (2) ovarian stroma, benign ovarian tumors (3), low grade (4) and high grade (5) serous tumors, and endometrioid tumors (6). We developed a tailored set of 3D filters which extract textural features in the 3D image sets to build (or learn) statistical models of each tissue class. By applying k-nearest neighbor classification using these learned models, we achieved 83–91% accuracies for the six classes. The 3D method outperformed the analogous 2D classification on the same tissues, where we suggest this is due the increased information content. This classification based on ECM structural changes will complement conventional classification based on genetic profiles and can serve as an additional biomarker. Moreover, the texture analysis algorithm is quite general, as it does not rely on single morphological metrics such as fiber alignment, length, and width but their combined convolution with a customizable basis set. PMID:27767180

  10. Effects of 3D PIV post-processing on impulse and force analysis in vortical flows

    NASA Astrophysics Data System (ADS)

    Mendelson, Leah; Techet, Alexandra

    2014-11-01

    Vortical flows measured using 3D PIV techniques are fundamentally filtered versions of physical phenomena, with velocity information lost below the length and time scales of the measurement system. In the context of propulsive vortices, such as those generated during biological locomotion, these factors, combined with experimental noise and error, can lead to inaccuracies in analysis of the vortex momentum and net thrust. As a result, while 3D velocity measurements remove many of the assumptions required to analyze planar PIV data, they should not be considered absolute physical quantities. Our work focuses on post-processing for 3D PIV data sets to enable the extraction of accurate, quantitative 3D force measurements for unsteady vortical propulsion. In this study, we compare utilizing measurement signal processing techniques, orthogonal decomposition, and identification of coherent structures to measure the impulse of a canonical vortex ring generated by a mechanical piston. In particular, we consider the ability of these methods to confront the influences of limited spatial resolution and arbitrary geometries, and make recommendations for a general procedure for propulsion analysis from 3D PIV data, regardless of which PIV technique is used to obtain the velocity fields.

  11. Using "click-e-bricks" to make 3D elastomeric structures.

    PubMed

    Morin, Stephen A; Shevchenko, Yanina; Lessing, Joshua; Kwok, Sen Wai; Shepherd, Robert F; Stokes, Adam A; Whitesides, George M

    2014-09-10

    Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.

  12. The 3D velocity structure beneath Iceland: Identifying melt pathways

    NASA Astrophysics Data System (ADS)

    Allen, R.

    2003-04-01

    The integration of various seismic datasets, recorded by the broadband HOTSPOT network deployed across Iceland, provides one of the highest resolution studies of the crust and mantle structure associated with a plume-ridge system. The mantle P- and S-velocity models (ICEMAN), derived from teleseismic body-wave and surface wave analysis, show a vertical, cylindrical low velocity anomaly ˜200 km in diameter extending from ˜400 km, the maximum depth of resolution, up to ˜200 km above which low velocity material is present beneath all of Iceland. The maximum P- and S-velocity anomalies of -2% and -4% respectively are found beneath the northwestern edge of Vatnajokull. The crustal S-velocity model (ICECRTb) is constrained by local surface waves, refraction experiments and receiver functions, and shows significant variation in crustal thickness. The thinnest, ˜15 km, crust is found around coastal regions, the thickest crust is beneath northwestern Vatnajokull where it reaches a thickness of 45 km. Within this thick crustal root is a vertical low velocity anomaly connecting the core of the mantle anomaly to horizontal low velocity regions that extend along the western and eastern volcanic zones but not the northern volcanic zone. These crustal low velocity zones are interpreted as regions through which melt is fed from the mantle to shallow magma chambers beneath the rift zones, where crustal formation occurs. The pipework between the core of the mantle anomaly and the southern rift zones is responsible for ˜30 km thick crust. Its absence to the north results in relatively thin, ˜20 km thick, crust.

  13. MAP(2.0)3D: a sequence/structure based server for protein engineering.

    PubMed

    Verma, Rajni; Schwaneberg, Ulrich; Roccatano, Danilo

    2012-04-20

    The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.

  14. 3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

    PubMed

    Via, Allegra; Peluso, Daniele; Gherardini, Pier Federico; de Rinaldis, Emanuele; Colombo, Teresa; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2007-07-01

    3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/ PMID:17488847

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

    PubMed

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

    2016-07-01

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

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

    PubMed Central

    Pei, Jimin; Grishin, Nick V.

    2015-01-01

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

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

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

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

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

    PubMed

    Pei, Jimin; Grishin, Nick V

    2014-01-01

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

  19. Finite element analysis of 3D elastic-plastic frictional contact problem for Cosserat materials

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Xie, Z. Q.; Chen, B. S.; Zhang, H. W.

    2013-06-01

    The objective of this paper is to develop a finite element model for 3D elastic-plastic frictional contact problem of Cosserat materials. Because 3D elastic-plastic frictional contact problems belong to the unspecified boundary problems with nonlinearities in both material and geometric forms, a large number of calculations are needed to obtain numerical results with high accuracy. Based on the parametric variational principle and the corresponding quadratic programming method for numerical simulation of frictional contact problems, a finite element model is developed for 3D elastic-plastic frictional contact analysis of Cosserat materials. The problems are finally reduced to linear complementarity problems (LCP). Numerical examples show the feasibility and importance of the developed model for analyzing the contact problems of structures with materials which have micro-polar characteristics.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

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

  2. The 3D Structure of the Galactic Bulge

    NASA Astrophysics Data System (ADS)

    Zoccali, Manuela; Valenti, Elena

    2016-06-01

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

  3. Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

    PubMed Central

    Buchan, Daniel W.A.; Shepherd, Adrian J.; Lee, David; Pearl, Frances M.G.; Rison, Stuart C.G.; Thornton, Janet M.; Orengo, Christine A.

    2002-01-01

    We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies. PMID:11875040

  4. Micro-CT for the quantification of 3D voids within damaged structures

    SciTech Connect

    Patterson, Brian M; Hamilton, Christopher E; Cerreta, Ellen K; Dennis - Koller, Darcie; Bronkhorst, C. A.; Hansen, B. L.

    2011-01-26

    Micro X-ray Computed Tomography (MXCT) is widely used in the materials community to examine the internal structure of materials for voids and cracks due to damage or casting, or other defects. Most research in this area focuses on the qualitative aspect of the image, simply answering; Are there voids present? Here we present an ongoing study of the quantified incipient spall voids in Cu with different grain sizes, using a gas gun with various velocities. Data analysis packages for MXCT are just now becoming able to dimensionally measure and produce statistics on the voids-present. In order to make the size of the features in the 3D image quantifiable, the question, how many radiographs are required to render the object dimensionally accurate in 3D, must be answered. A series of data sets has been coUected, varying the number of radiographs collected in order to determine the appropriate number required.

  5. 3D image analysis of abdominal aortic aneurysm

    NASA Astrophysics Data System (ADS)

    Subasic, Marko; Loncaric, Sven; Sorantin, Erich

    2002-05-01

    This paper presents a method for 3-D segmentation of abdominal aortic aneurysm from computed tomography angiography images. The proposed method is automatic and requires minimal user assistance. Segmentation is performed in two steps. First inner and then outer aortic border is segmented. Those two steps are different due to different image conditions on two aortic borders. Outputs of these two segmentations give a complete 3-D model of abdominal aorta. Such a 3-D model is used in measurements of aneurysm area. The deformable model is implemented using the level-set algorithm due to its ability to describe complex shapes in natural manner which frequently occur in pathology. In segmentation of outer aortic boundary we introduced some knowledge based preprocessing to enhance and reconstruct low contrast aortic boundary. The method has been implemented in IDL and C languages. Experiments have been performed using real patient CTA images and have shown good results.

  6. Minimizing camera-eye optical aberrations during the 3D reconstruction of retinal structures

    NASA Astrophysics Data System (ADS)

    Aldana-Iuit, Javier; Martinez-Perez, M. Elena; Espinosa-Romero, Arturo; Diaz-Uribe, Rufino

    2010-05-01

    3D reconstruction of blood vessels is a powerful visualization tool for physicians, since it allows them to refer to qualitative representation of their subject of study. In this paper we propose a 3D reconstruction method of retinal vessels from fundus images. The reconstruction method propose herein uses images of the same retinal structure in epipolar geometry. Images are preprocessed by RISA system for segmenting blood vessels and obtaining feature points for correspondences. The correspondence points process is solved using correlation. The LMedS analysis and Graph Transformation Matching algorithm are used for outliers suppression. Camera projection matrices are computed with the normalized eight point algorithm. Finally, we retrieve 3D position of the retinal tree points by linear triangulation. In order to increase the power of visualization, 3D tree skeletons are represented by surfaces via generalized cylinders whose radius correspond to morphological measurements obtained by RISA. In this paper the complete calibration process including the fundus camera and the optical properties of the eye, the so called camera-eye system is proposed. On one hand, the internal parameters of the fundus camera are obtained by classical algorithms using a reference pattern. On the other hand, we minimize the undesirable efects of the aberrations induced by the eyeball optical system assuming that contact enlarging lens corrects astigmatism, spherical and coma aberrations are reduced changing the aperture size and eye refractive errors are suppressed adjusting camera focus during image acquisition. Evaluation of two self-calibration proposals and results of 3D blood vessel surface reconstruction are presented.

  7. 3D statistical failure analysis of monolithic dental ceramic crowns.

    PubMed

    Nasrin, Sadia; Katsube, Noriko; Seghi, Robert R; Rokhlin, Stanislav I

    2016-07-01

    For adhesively retained ceramic crown of various types, it has been clinically observed that the most catastrophic failures initiate from the cement interface as a result of radial crack formation as opposed to Hertzian contact stresses originating on the occlusal surface. In this work, a 3D failure prognosis model is developed for interface initiated failures of monolithic ceramic crowns. The surface flaw distribution parameters determined by biaxial flexural tests on ceramic plates and point-to-point variations of multi-axial stress state at the intaglio surface are obtained by finite element stress analysis. They are combined on the basis of fracture mechanics based statistical failure probability model to predict failure probability of a monolithic crown subjected to single-cycle indentation load. The proposed method is verified by prior 2D axisymmetric model and experimental data. Under conditions where the crowns are completely bonded to the tooth substrate, both high flexural stress and high interfacial shear stress are shown to occur in the wall region where the crown thickness is relatively thin while high interfacial normal tensile stress distribution is observed at the margin region. Significant impact of reduced cement modulus on these stress states is shown. While the analyses are limited to single-cycle load-to-failure tests, high interfacial normal tensile stress or high interfacial shear stress may contribute to degradation of the cement bond between ceramic and dentin. In addition, the crown failure probability is shown to be controlled by high flexural stress concentrations over a small area, and the proposed method might be of some value to detect initial crown design errors. PMID:27215334

  8. 3D statistical failure analysis of monolithic dental ceramic crowns.

    PubMed

    Nasrin, Sadia; Katsube, Noriko; Seghi, Robert R; Rokhlin, Stanislav I

    2016-07-01

    For adhesively retained ceramic crown of various types, it has been clinically observed that the most catastrophic failures initiate from the cement interface as a result of radial crack formation as opposed to Hertzian contact stresses originating on the occlusal surface. In this work, a 3D failure prognosis model is developed for interface initiated failures of monolithic ceramic crowns. The surface flaw distribution parameters determined by biaxial flexural tests on ceramic plates and point-to-point variations of multi-axial stress state at the intaglio surface are obtained by finite element stress analysis. They are combined on the basis of fracture mechanics based statistical failure probability model to predict failure probability of a monolithic crown subjected to single-cycle indentation load. The proposed method is verified by prior 2D axisymmetric model and experimental data. Under conditions where the crowns are completely bonded to the tooth substrate, both high flexural stress and high interfacial shear stress are shown to occur in the wall region where the crown thickness is relatively thin while high interfacial normal tensile stress distribution is observed at the margin region. Significant impact of reduced cement modulus on these stress states is shown. While the analyses are limited to single-cycle load-to-failure tests, high interfacial normal tensile stress or high interfacial shear stress may contribute to degradation of the cement bond between ceramic and dentin. In addition, the crown failure probability is shown to be controlled by high flexural stress concentrations over a small area, and the proposed method might be of some value to detect initial crown design errors.

  9. 3-D Structure of Molecules of Biological Significance

    ERIC Educational Resources Information Center

    Bennett, Alice S.; Schwenk, Karl

    1974-01-01

    Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

  10. MUFOLD: A new solution for protein 3D structure prediction

    PubMed Central

    Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

    2010-01-01

    There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the Cα or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8. PMID:19927325

  11. Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

    NASA Astrophysics Data System (ADS)

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-03-01

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

  12. Subtractive 3D printing of optically active diamond structures.

    PubMed

    Martin, Aiden A; Toth, Milos; Aharonovich, Igor

    2014-05-21

    Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

  13. Characterization of ABS specimens produced via the 3D printing technology for drone structural components

    NASA Astrophysics Data System (ADS)

    Ferro, Carlo Giovanni; Brischetto, Salvatore; Torre, Roberto; Maggiore, Paolo

    2016-07-01

    The Fused Deposition Modelling (FDM) technology is widely used in rapid prototyping. 3D printers for home desktop applications are usually employed to make non-structural objects. When the mechanical stresses are not excessive, this technology can also be successfully employed to produce structural objects, not only in prototyping stage but also in the realization of series pieces. The innovative idea of the present work is the application of this technology, implemented in a desktop 3D printer, to the realization of components for aeronautical use, especially for unmanned aerial systems. For this purpose, the paper is devoted to the statistical study of the performance of a desktop 3D printer to understand how the process performs and which are the boundary limits of acceptance. Mechanical and geometrical properties of ABS (Acrylonitrile Butadiene Styrene) specimens, such as tensile strength and stiffness, have been evaluated. ASTM638 type specimens have been used. A capability analysis has been applied for both mechanical and dimensional performances. Statistically stable limits have been determined using experimentally collected data.

  14. Hybrid segmentation framework for 3D medical image analysis

    NASA Astrophysics Data System (ADS)

    Chen, Ting; Metaxas, Dimitri N.

    2003-05-01

    Medical image segmentation is the process that defines the region of interest in the image volume. Classical segmentation methods such as region-based methods and boundary-based methods cannot make full use of the information provided by the image. In this paper we proposed a general hybrid framework for 3D medical image segmentation purposes. In our approach we combine the Gibbs Prior model, and the deformable model. First, Gibbs Prior models are applied onto each slice in a 3D medical image volume and the segmentation results are combined to a 3D binary masks of the object. Then we create a deformable mesh based on this 3D binary mask. The deformable model will be lead to the edge features in the volume with the help of image derived external forces. The deformable model segmentation result can be used to update the parameters for Gibbs Prior models. These methods will then work recursively to reach a global segmentation solution. The hybrid segmentation framework has been applied to images with the objective of lung, heart, colon, jaw, tumor, and brain. The experimental data includes MRI (T1, T2, PD), CT, X-ray, Ultra-Sound images. High quality results are achieved with relatively efficient time cost. We also did validation work using expert manual segmentation as the ground truth. The result shows that the hybrid segmentation may have further clinical use.

  15. PROP3D: A Program for 3D Euler Unsteady Aerodynamic and Aeroelastic (Flutter and Forced Response) Analysis of Propellers. Version 1.0

    NASA Technical Reports Server (NTRS)

    Srivastava, R.; Reddy, T. S. R.

    1996-01-01

    This guide describes the input data required, for steady or unsteady aerodynamic and aeroelastic analysis of propellers and the output files generated, in using PROP3D. The aerodynamic forces are obtained by solving three dimensional unsteady, compressible Euler equations. A normal mode structural analysis is used to obtain the aeroelastic equations, which are solved using either time domain or frequency domain solution method. Sample input and output files are included in this guide for steady aerodynamic analysis of single and counter-rotation propellers, and aeroelastic analysis of single-rotation propeller.

  16. Delineation of nuclear structures in 3D multicellular systems

    SciTech Connect

    2013-09-13

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

  17. Imaging solar coronal magnetic structures in 3D

    NASA Astrophysics Data System (ADS)

    Cartledge, N. P.

    The study of solar coronal structures and, in particular prominences, is a key part of understanding the highly complex physical mechanisms occurring in the Sun's atmosphere. Solar prominences are important in their own right and some of the most puzzling questions in solar theory have arisen through their study. For example, how do they form and how is their mass continuously replenished? How can the magnetic field provide their continuous support against gravity over time periods of several months? How can such cool, dense material exist in thermal equilibrium in the surrounding coronal environment? Why do they erupt? A study of their structure and that of the surrounding medium is important in determining the nature of the coronal plasma and magnetic field. Also, prominences are closely associated with other key phenomena such as coronal mass ejections and eruptive solar flares which occur as a prominence loses equilibrium and rises from the solar surface. Our current understanding of these fascinating structures is extremely limited and we know very little about their basic global structure. In fact, recent prominence observations have caused our basic paradigms to be challenged (Priest, 1996) and so we must set up new models in order to gain even a fundamental understanding. Prominences are highly nonlinear, three-dimensional structures. Large feet (or barbs) reach out from the main body of a prominence and reach down to the photosphere where the dense material continuously drains away. These provide a real clue to the three-dimensional nature of the coronal field and its relation to the photospheric field. It is important, therefore, to make stereographic observations of prominences in order to gain a basic understanding of their essentially three-dimensional nature and attempt to formulate new paradigms for their structure and evolution. There is no doubt that the study of prominences in three dimensions is a crucial exercise if we are to develop a better

  18. Designing self-assembling 3D structures of microcapsules

    NASA Astrophysics Data System (ADS)

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

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

  19. 3D Printing for Spacecraft Multi-Functional Structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  20. Value of Computerized 3D Shape Analysis in Differentiating Encapsulated from Invasive Thymomas

    PubMed Central

    Lee, Jong Hyuk; Park, Chang Min; Park, Sang Joon; Bae, Jae Seok; Lee, Sang Min; Goo, Jin Mo

    2015-01-01

    Objectives To retrospectively investigate the added value of quantitative 3D shape analysis in differentiating encapsulated from invasive thymomas. Materials and Methods From February 2002 to October 2013, 53 patients (25 men and 28 women; mean age, 53.94 ± 13.13 years) with 53 pathologically-confirmed thymomas underwent preoperative chest CT scans (slice thicknesses ≤ 2.5 mm). Twenty-three tumors were encapsulated thymomas and 30 were invasive thymomas. Their clinical and CT characteristics were evaluated. In addition, each thymoma was manually-segmented from surrounding structures, and their 3D shape features were assessed using an in-house developed software program. To evaluate the added value of 3D shape features in differentiating encapsulated from invasive thymomas, logistic regression analysis and receiver-operating characteristics curve (ROC) analysis were performed. Results Significant differences were observed between encapsulated and invasive thymomas, in terms of cystic changes (p=0.004), sphericity (p=0.016), and discrete compactness (p=0.001). Subsequent binary logistic regression analysis revealed that absence of cystic change (adjusted odds ratio (OR) = 6.636; p=0.015) and higher discrete compactness (OR = 77.775; p=0.012) were significant differentiators of encapsulated from invasive thymomas. ROC analyses revealed that the addition of 3D shape analysis to clinical and CT features (AUC, 0.955; 95% CI, 0.935–0.975) provided significantly higher performance in differentiating encapsulated from invasive thymomas than clinical and CT features (AUC, 0.666; 95% CI, 0.626–0.707) (p<0.001). Conclusion Addition of 3D shape analysis, particularly discrete compactness, can improve differentiation of encapsulated thymomas from invasive thymomas. PMID:25938505

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

    PubMed Central

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    PubMed

    Wang, Jianwei; Zhang, Yong

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Jianwei; Zhang, Yong

    2016-04-01

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

  4. Determining the 3-D structure and motion of objects using a scanning laser range sensor

    NASA Technical Reports Server (NTRS)

    Nandhakumar, N.; Smith, Philip W.

    1993-01-01

    In order for the EVAHR robot to autonomously track and grasp objects, its vision system must be able to determine the 3-D structure and motion of an object from a sequence of sensory images. This task is accomplished by the use of a laser radar range sensor which provides dense range maps of the scene. Unfortunately, the currently available laser radar range cameras use a sequential scanning approach which complicates image analysis. Although many algorithms have been developed for recognizing objects from range images, none are suited for use with single beam, scanning, time-of-flight sensors because all previous algorithms assume instantaneous acquisition of the entire image. This assumption is invalid since the EVAHR robot is equipped with a sequential scanning laser range sensor. If an object is moving while being imaged by the device, the apparent structure of the object can be significantly distorted due to the significant non-zero delay time between sampling each image pixel. If an estimate of the motion of the object can be determined, this distortion can be eliminated; but, this leads to the motion-structure paradox - most existing algorithms for 3-D motion estimation use the structure of objects to parameterize their motions. The goal of this research is to design a rigid-body motion recovery technique which overcomes this limitation. The method being developed is an iterative, linear, feature-based approach which uses the non-zero image acquisition time constraint to accurately recover the motion parameters from the distorted structure of the 3-D range maps. Once the motion parameters are determined, the structural distortion in the range images is corrected.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  6. Shape analysis of corpus callosum in phenylketonuria using a new 3D correspondence algorithm

    NASA Astrophysics Data System (ADS)

    He, Qing; Christ, Shawn E.; Karsch, Kevin; Peck, Dawn; Duan, Ye

    2010-03-01

    Statistical shape analysis of brain structures has gained increasing interest from neuroimaging community because it can precisely locate shape differences between healthy and pathological structures. The most difficult and crucial problem is establishing shape correspondence among individual 3D shapes. This paper proposes a new algorithm for 3D shape correspondence. A set of landmarks are sampled on a template shape, and initial correspondence is established between the template and the target shape based on the similarity of locations and normal directions. The landmarks on the target are then refined by iterative thin plate spline. The algorithm is simple and fast, and no spherical mapping is needed. We apply our method to the statistical shape analysis of the corpus callosum (CC) in phenylketonuria (PKU), and significant local shape differences between the patients and the controls are found in the most anterior and posterior aspects of the corpus callosum.

  7. 3D nano-structures for laser nano-manipulation.

    PubMed

    Seniutinas, Gediminas; Rosa, Lorenzo; Gervinskas, Gediminas; Brasselet, Etienne; Juodkazis, Saulius

    2013-01-01

    The resputtering of gold films from nano-holes defined in a sacrificial PMMA mask, which was made by electron beam lithography, was carried out with a dry plasma etching tool in order to form well-like structures with a high aspect ratio (height/width ≈ 3-4) at the rims of the nano-holes. The extraordinary transmission through the patterns of such nano-wells was investigated experimentally and numerically. By doing numerical simulations of 50-nm and 100-nm diameter polystyrene beads in water and air, we show the potential of such patterns for self-induced back-action (SIBA) trapping. The best trapping conditions were found to be a trapping force of 2 pN/W/μm(2) (numerical result) exerted on a 50-nm diameter bead in water. The simulations were based on the analytical Lorentz force model.

  8. Monte Carlo generators for studies of the 3D structure of the nucleon

    DOE PAGES

    Avakian, Harut; D'Alesio, U.; Murgia, F.

    2015-01-23

    In this study, extraction of transverse momentum and space distributions of partons from measurements of spin and azimuthal asymmetries requires development of a self consistent analysis framework, accounting for evolution effects, and allowing control of systematic uncertainties due to variations of input parameters and models. Development of realistic Monte-Carlo generators, accounting for TMD evolution effects, spin-orbit and quark-gluon correlations will be crucial for future studies of quark-gluon dynamics in general and 3D structure of the nucleon in particular.

  9. 3d Modeling of cultural heritage objects with a structured light system.

    NASA Astrophysics Data System (ADS)

    Akca, Devrim

    3D modeling of cultural heritage objects is an expanding application area. The selection of the right technology is very important and strictly related to the project requirements, budget and user's experience. The triangulation based active sensors, e.g. structured light systems are used for many kinds of 3D object reconstruction tasks and in particular for 3D recording of cultural heritage objects. This study presents the experiences in the results of two such projects in which a close-range structured light system is used for the 3D digitization. The paper includes the essential steps of the 3D object modeling pipeline, i.e. digitization, registration, surface triangulation, editing, texture mapping and visualization. The capabilities of the used hardware and software are addressed. Particular emphasis is given to a coded structured light system as an option for data acquisition.

  10. Electrodeposition-based 3D Printing of Metallic Microarchitectures with Controlled Internal Structures.

    PubMed

    Seol, Seung Kwon; Kim, Daeho; Lee, Sanghyeon; Kim, Jung Hyun; Chang, Won Suk; Kim, Ji Tae

    2015-08-26

    3D printing of metallic microarchitectures with controlled internal structures is realized at room temperature in ambient air conditions by the manipulation of metal ion concentration and pulsed electric potentials in the electrolyte meniscus during the meniscus-guided electrodeposition. Precise control of the printing nozzle enables the drawing of complex 3D microarchitectures with well-defined geometries and positions. PMID:25917532

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. Global stability analysis of turbulent 3D wakes

    NASA Astrophysics Data System (ADS)

    Rigas, Georgios; Sipp, Denis; Juniper, Matthew

    2015-11-01

    At low Reynolds numbers, corresponding to laminar and transitional regimes, hydrodynamic stability theory has aided the understanding of the dynamics of bluff body wake-flows and the application of effective control strategies. However, flows of fundamental importance to many industries, in particular the transport industry, involve high Reynolds numbers and turbulent wakes. Despite their turbulence, such wake flows exhibit organisation which is manifested as coherent structures. Recent work has shown that the turbulent coherent structures retain the shape of the symmetry-breaking laminar instabilities and only those manifest as large-scale structures in the near wake (Rigas et al., JFM vol. 750:R5 2014, JFM vol. 778:R2 2015). Based on the findings of the persistence of the laminar instabilities at high Reynolds numbers, we investigate the global stability characteristics of a turbulent wake generated behind a bluff three-dimensional axisymmetric body. We perform a linear global stability analysis on the experimentally obtained mean flow and we recover the dynamic characteristics and spatial structure of the coherent structures, which are linked to the transitional instabilities. A detailed comparison of the predictions with the experimental measurements will be provided.

  13. 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.

  14. 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

  15. High-resolution 3D micro-CT imaging of breast microcalcifications: a preliminary analysis

    PubMed Central

    2014-01-01

    Background Detection of microcalcifications on mammograms indicates the presence of breast lesion, and the shapes of the microcalcifications as seen by conventional mammography correlates with the probability of malignancy. This preliminary study evaluated the 3D shape of breast microcalcifications using micro-computed tomography (micro-CT) and compared the findings with those obtained using anatomopathological analysis. Methods The study analyzed breast biopsy samples from 11 women with findings of suspicious microcalcifications on routine mammograms. The samples were imaged using a micro-CT (SkyScan 1076) at a resolution of 35 μm. Images were reconstructed using filtered back-projection and analyzed in 3D using surface rendering. The samples were subsequently analyzed by the pathology service. Reconstructed 3D images were compared with the corresponding histological slices. Results Anatomopathological analysis showed that 5 of 11 patients had ductal breast carcinoma in situ. One patient was diagnosed with invasive ductal carcinoma. Individual object analysis was performed on 597 microcalcifications. Malignant microcalcifications tended to be thinner and to have a smaller volume and surface area, while their surface area-to-volume ratio was greater than that of benign microcalcifications. The structure model index values were the same for malignant and benign microcalcifications. Conclusions This is the first study to use micro-CT for quantitative 3D analysis of microcalcifications. This high-resolution imaging technique will be valuable for gaining a greater understanding of the morphologic characteristics of malignant and benign microcalcifications. The presence of many small microcalcifications can be an indication of malignancy. For the larger microcalcifications, 3D parameters confirmed the more irregular shape of malignant microcalcifications. PMID:24393444

  16. 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).

  17. Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

    PubMed Central

    Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

    2014-01-01

    Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports

  18. Sequence co-evolution gives 3D contacts and structures of protein complexes

    PubMed Central

    Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

    2014-01-01

    Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

  19. Importance of a 3D forward modeling tool for surface wave analysis methods

    NASA Astrophysics Data System (ADS)

    Pageot, Damien; Le Feuvre, Mathieu; Donatienne, Leparoux; Philippe, Côte; Yann, Capdeville

    2016-04-01

    Since a few years, seismic surface waves analysis methods (SWM) have been widely developed and tested in the context of subsurface characterization and have demonstrated their effectiveness for sounding and monitoring purposes, e.g., high-resolution tomography of the principal geological units of California or real time monitoring of the Piton de la Fournaise volcano. Historically, these methods are mostly developed under the assumption of semi-infinite 1D layered medium without topography. The forward modeling is generally based on Thomson-Haskell matrix based modeling algorithm and the inversion is driven by Monte-Carlo sampling. Given their efficiency, SWM have been transfered to several scale of which civil engineering structures in order to, e.g., determine the so-called V s30 parameter or assess other critical constructional parameters in pavement engineering. However, at this scale, many structures may often exhibit 3D surface variations which drastically limit the efficiency of SWM application. Indeed, even in the case of an homogeneous structure, 3D geometry can bias the dispersion diagram of Rayleigh waves up to obtain discontinuous phase velocity curves which drastically impact the 1D mean velocity model obtained from dispersion inversion. Taking advantages of high-performance computing center accessibility and wave propagation modeling algorithm development, it is now possible to consider the use of a 3D elastic forward modeling algorithm instead of Thomson-Haskell method in the SWM inversion process. We use a parallelized 3D elastic modeling code based on the spectral element method which allows to obtain accurate synthetic data with very low numerical dispersion and a reasonable numerical cost. In this study, we choose dike embankments as an illustrative example. We first show that their longitudinal geometry may have a significant effect on dispersion diagrams of Rayleigh waves. Then, we demonstrate the necessity of 3D elastic modeling as a forward

  20. 3D printing meets computational astrophysics: deciphering the structure of η Carinae's inner colliding winds

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  1. Exome-Scale Discovery of Hotspot Mutation Regions in Human Cancer Using 3D Protein Structure.

    PubMed

    Tokheim, Collin; Bhattacharya, Rohit; Niknafs, Noushin; Gygax, Derek M; Kim, Rick; Ryan, Michael; Masica, David L; Karchin, Rachel

    2016-07-01

    The impact of somatic missense mutation on cancer etiology and progression is often difficult to interpret. One common approach for assessing the contribution of missense mutations in carcinogenesis is to identify genes mutated with statistically nonrandom frequencies. Even given the large number of sequenced cancer samples currently available, this approach remains underpowered to detect drivers, particularly in less studied cancer types. Alternative statistical and bioinformatic approaches are needed. One approach to increase power is to focus on localized regions of increased missense mutation density or hotspot regions, rather than a whole gene or protein domain. Detecting missense mutation hotspot regions in three-dimensional (3D) protein structure may also be beneficial because linear sequence alone does not fully describe the biologically relevant organization of codons. Here, we present a novel and statistically rigorous algorithm for detecting missense mutation hotspot regions in 3D protein structures. We analyzed approximately 3 × 10(5) mutations from The Cancer Genome Atlas (TCGA) and identified 216 tumor-type-specific hotspot regions. In addition to experimentally determined protein structures, we considered high-quality structural models, which increase genomic coverage from approximately 5,000 to more than 15,000 genes. We provide new evidence that 3D mutation analysis has unique advantages. It enables discovery of hotspot regions in many more genes than previously shown and increases sensitivity to hotspot regions in tumor suppressor genes (TSG). Although hotspot regions have long been known to exist in both TSGs and oncogenes, we provide the first report that they have different characteristic properties in the two types of driver genes. We show how cancer researchers can use our results to link 3D protein structure and the biologic functions of missense mutations in cancer, and to generate testable hypotheses about driver mechanisms. Our results

  2. Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) for a 3-D Flexible Wing

    NASA Technical Reports Server (NTRS)

    Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.

    2001-01-01

    The formulation and implementation of an optimization method called Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) are extended from single discipline analysis (aerodynamics only) to multidisciplinary analysis - in this case, static aero-structural analysis and applied to a simple 3-D wing problem. The method aims to reduce the computational expense incurred in performing shape optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, Finite Element Method (FEM) structural analysis and sensitivity analysis tools. Results for this small problem show that the method reaches the same local optimum as conventional optimization. However, unlike its application to the rigid wing (single discipline analysis), the method, as implemented here, may not show significant reduction in the computational cost. Similar reductions were seen in the two-design-variable (DV) problem results but not in the 8-DV results given here.

  3. Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) for a 3-D Flexible Wing

    NASA Technical Reports Server (NTRS)

    Gumbert, Clyde R.; Hou, Gene J.-W.

    2001-01-01

    The formulation and implementation of an optimization method called Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) are extended from single discipline analysis (aerodynamics only) to multidisciplinary analysis - in this case, static aero-structural analysis - and applied to a simple 3-D wing problem. The method aims to reduce the computational expense incurred in performing shape optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, Finite Element Method (FEM) structural analysis and sensitivity analysis tools. Results for this small problem show that the method reaches the same local optimum as conventional optimization. However, unlike its application to the win,, (single discipline analysis), the method. as I implemented here, may not show significant reduction in the computational cost. Similar reductions were seen in the two-design-variable (DV) problem results but not in the 8-DV results given here.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Weinekoetter, Christian

    2008-09-01

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

  6. Customisable 3D printed microfluidics for integrated analysis and optimisation.

    PubMed

    Monaghan, T; Harding, M J; Harris, R A; Friel, R J; Christie, S D R

    2016-08-16

    The formation of smart Lab-on-a-Chip (LOC) devices featuring integrated sensing optics is currently hindered by convoluted and expensive manufacturing procedures. In this work, a series of 3D-printed LOC devices were designed and manufactured via stereolithography (SL) in a matter of hours. The spectroscopic performance of a variety of optical fibre combinations were tested, and the optimum path length for performing Ultraviolet-visible (UV-vis) spectroscopy determined. The information gained in these trials was then used in a reaction optimisation for the formation of carvone semicarbazone. The production of high resolution surface channels (100-500 μm) means that these devices were capable of handling a wide range of concentrations (9 μM-38 mM), and are ideally suited to both analyte detection and process optimisation. This ability to tailor the chip design and its integrated features as a direct result of the reaction being assessed, at such a low time and cost penalty greatly increases the user's ability to optimise both their device and reaction. As a result of the information gained in this investigation, we are able to report the first instance of a 3D-printed LOC device with fully integrated, in-line monitoring capabilities via the use of embedded optical fibres capable of performing UV-vis spectroscopy directly inside micro channels. PMID:27452498

  7. Wear Analysis of Thermal Spray Coatings on 3D Surfaces

    NASA Astrophysics Data System (ADS)

    Tillmann, W.; Luo, W.; Selvadurai, U.

    2014-01-01

    Even though the application of thermal spray coatings on complex geometries gained a greater interest in the last decade, the effect of different geometrical features on the wear behavior is still ill-defined. In this study, the wear resistance of FTC-FeCSiMn coated 3D surfaces was investigated. The wear test was carried out by means of two innovative testing procedures. The first test is a Pin-on-Tubes test where the rotating motion is realized by a lathe chuck. The specimens in the second test were fixed on the table and a robot arm operated the pin. This wear test was applied on specimens with concave or convex surfaces. The residual stresses, which were determined by means of an incremental hole-drilling method, show a dependency on the substrate geometry. The obtained stresses were put in relation to the different radii. After the wear test, a 3D-profilometer determined the wear volume and the sections of the coatings were characterized by a scanning electron microscope. The results indicate that the wear resistance is strongly influenced by the geometry of the substrate.

  8. Metrological analysis of the human foot: 3D multisensor exploration

    NASA Astrophysics Data System (ADS)

    Muñoz Potosi, A.; Meneses Fonseca, J.; León Téllez, J.

    2011-08-01

    In the podiatry field, many of the foot dysfunctions are mainly generated due to: Congenital malformations, accidents or misuse of footwear. For the treatment or prevention of foot disorders, the podiatrist diagnoses prosthesis or specific adapted footwear, according to the real dimension of foot. Therefore, it is necessary to acquire 3D information of foot with 360 degrees of observation. As alternative solution, it was developed and implemented an optical system of threedimensional reconstruction based in the principle of laser triangulation. The system is constituted by an illumination unit that project a laser plane into the foot surface, an acquisition unit with 4 CCD cameras placed around of axial foot axis, an axial moving unit that displaces the illumination and acquisition units in the axial axis direction and a processing and exploration unit. The exploration software allows the extraction of distances on three-dimensional image, taking into account the topography of foot. The optical system was tested and their metrological performances were evaluated in experimental conditions. The optical system was developed to acquire 3D information in order to design and make more appropriate footwear.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Complex Crustal Structure Beneath Western Turkey Revealed by 3D Seismic Full Waveform Inversion (FWI)

    NASA Astrophysics Data System (ADS)

    Cubuk-Sabuncu, Yesim; Taymaz, Tuncay; Fichtner, Andreas

    2016-04-01

    We present a 3D radially anisotropic velocity model of the crust and uppermost mantle structure beneath the Sea of Marmara and surroundings based on the full waveform inversion method. The intense seismic activity and crustal deformation are observed in the Northwest Turkey due to transition tectonics between the strike-slip North Anatolian Fault (NAF) and the extensional Aegean region. We have selected and simulated complete waveforms of 62 earthquakes (Mw > 4.0) occurred during 2007-2015, and recorded at (Δ < 10°) distances. Three component earthquake data is obtained from broadband seismic stations of Kandilli Observatory and Earthquake Research Center (KOERI, Turkey), Hellenic Unified Seismic Network (HUSN, Greece) and Earthquake Research Center of Turkey (AFAD-DAD). The spectral-element solver of the wave equation, SES3D algorithm, is used to simulate seismic wave propagation in 3D spherical coordinates (Fichtner, 2009). The Large Scale Seismic Inversion Framework (LASIF) workflow tool is also used to perform full seismic waveform inversion (Krischer et al., 2015). The initial 3D Earth model is implemented from the multi-scale seismic tomography study of Fichtner et al. (2013). Discrepancies between the observed and simulated synthetic waveforms are determined using the time-frequency misfits which allows a separation between phase and amplitude information (Fichtner et al., 2008). The conjugate gradient optimization method is used to iteratively update the initial Earth model when minimizing the misfit. The inversion is terminated after 19 iterations since no further advances are observed in updated models. Our analysis revealed shear wave velocity variations of the shallow and deeper crustal structure beneath western Turkey down to depths of ~35-40 km. Low shear wave velocity anomalies are observed in the upper and mid crustal depths beneath major fault zones located in the study region. Low velocity zones also tend to mark the outline of young volcanic

  11. Waves of 3D marine structures slamming at different initial poses in complex wind-wave-flow environments

    NASA Astrophysics Data System (ADS)

    Zhu, Liang-sheng; Yu, Long-fei

    2016-10-01

    Aimed at the hydrodynamic response for marine structures slamming into water, based on the mechanism analysis to the slamming process, and by combining 3D N-S equation and k- ɛ turbulent kinetic equation with structure fully 6DOF motion equation, a mathematical model for the wind-fluid-solid interaction is established in 3D marine structure slamming wave at free poses and wind-wave-flow complex environments. Compared with the results of physical model test, the numerical results from the slamming wave well correspond with the experimental results. Through the mathematical model, the wave-making issue of 3D marine structure at initial pose falls into water in different complex wind, wave and flow environments is investigated. The research results show that various kinds of natural factors and structure initial poses have different influence on the slamming wave, and there is an obvious rule in this process.

  12. Mu-Synthesis robust control of 3D bar structure vibration using piezo-stack actuators

    NASA Astrophysics Data System (ADS)

    Mystkowski, Arkadiusz; Koszewnik, Andrzej Piotr

    2016-10-01

    This paper presents an idea for the Mu-Synthesis robust control of 3D bar structure vibration with using a piezo-stack actuators. A model of the 3D bar structure with uncertain parameters is presented as multi-input multi-output (MIMO) dynamics. Nominal stability and nominal performances of the open-loop 3D bar structure dynamic model is developed. The uncertain model-based robust controller is derived due to voltage control signal saturation and selected parameter perturbations. The robust control performances and robustness of the system due to uncertainties influence is evaluated by using singular values and a small gain theorem. Finally, simulation investigations and experimental results shown that system response of the 3D bar structure dynamic model with taken into account perturbed parameters met desired robust stability and system limits. The proposed robust controller ensures a good dynamics of the closed-loop system, robustness, and vibration attenuation.

  13. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

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

  14. Active optical system for advanced 3D surface structuring by laser remelting

    NASA Astrophysics Data System (ADS)

    Pütsch, O.; Temmler, A.; Stollenwerk, J.; Willenborg, E.; Loosen, P.

    2015-03-01

    Structuring by laser remelting enables completely new possibilities for designing surfaces since material is redistributed but not wasted. In addition to technological advantages, cost and time benefits yield from shortened process times, the avoidance of harmful chemicals and the elimination of subsequent finishing steps such as cleaning and polishing. The functional principle requires a completely new optical machine technology that maintains the spatial and temporal superposition and manipulation of three different laser beams emitted from two laser sources of different wavelength. The optical system has already been developed and demonstrated for the processing of flat samples of hot and cold working steel. However, since particularly the structuring of 3D-injection molds represents an application example of high innovation potential, the optical system has to take into account the elliptical beam geometry that occurs when the laser beams irradiate a curved surface. To take full advantage of structuring by remelting for the processing of 3D surfaces, additional optical functionality, called EPS (elliptical pre-shaping) has to be integrated into the existing set-up. The development of the beam shaping devices not only requires the analysis of the mechanisms of the beam projection but also a suitable optical design. Both aspects are discussed in this paper.

  15. 3D velocity structure of upper crust beneath NW Bohemia/Vogtland

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  16. A 3D acquisition system combination of structured-light scanning and shape from silhouette

    NASA Astrophysics Data System (ADS)

    Sun, Changku; Tao, Li; Wang, Peng; He, Li

    2006-05-01

    A robust and accurate three dimensional (3D) acquisition system is presented, which is a combination of structured-light scanning and shape from silhouette. Using common world coordinate system, two groups of point data can be integrated into the final complete 3D model without any integration and registration algorithm. The mathematics model of structured-light scanning is described in detail, and the shape from silhouette algorithm is introduced as well. The complete 3D model of a cup with a handle is obtained successfully by the proposed technique. At last the measurement on a ball bearing is performed, with the measurement precision better than 0.15 mm.

  17. Analysis of patient movement during 3D USCT data acquisition

    NASA Astrophysics Data System (ADS)

    Ruiter, N. V.; Hopp, T.; Zapf, M.; Kretzek, E.; Gemmeke, H.

    2016-04-01

    In our first clinical study with a full 3D Ultrasound Computer Tomography (USCT) system patient data was acquired in eight minutes for one breast. In this paper the patient movement during the acquisition was analyzed quantitatively and as far as possible corrected in the resulting images. The movement was tracked in ten successive reflectivity reconstructions of full breast volumes acquired during 10 s intervals at different aperture positions, which were separated by 41 s intervals. The mean distance between initial and final position was 2.2 mm (standard deviation (STD) +/- 0.9 mm, max. 4.1 mm, min. 0.8 mm) and the average sum of all moved distances was 4.9 mm (STD +/- 1.9 mm, max. 8.8 mm, min. 2.7 mm). The tracked movement was corrected by summing successive images, which were transformed according to the detected movement. The contrast of these images increased and additional image content became visible.

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

    SciTech Connect

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

    2012-04-25

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

  19. The MHOST finite element program: 3-D inelastic analysis methods for hot section components. Volume 2: User's manual

    NASA Technical Reports Server (NTRS)

    Nakazawa, Shohei

    1989-01-01

    The user options available for running the MHOST finite element analysis package is described. MHOST is a solid and structural analysis program based on the mixed finite element technology, and is specifically designed for 3-D inelastic analysis. A family of 2- and 3-D continuum elements along with beam and shell structural elements can be utilized, many options are available in the constitutive equation library, the solution algorithms and the analysis capabilities. The outline of solution algorithms is discussed along with the data input and output, analysis options including the user subroutines and the definition of the finite elements implemented in the program package.

  20. Fit-sphere unwrapping and performance analysis of 3D fingerprints.

    PubMed

    Wang, Yongchang; Lau, Daniel L; Hassebrook, Laurence G

    2010-02-01

    To solve problems associated with conventional 2D fingerprint acquisition processes including skin deformations and print smearing, we developed a noncontact 3D fingerprint scanner employing structured light illumination that, in order to be backwards compatible with existing 2D fingerprint recognition systems, requires a method of unwrapping the 3D scans into 2D equivalent prints. For the latter purpose of virtually flattening a 3D print, this paper introduces a fit-sphere unwrapping algorithm. Taking advantage of detailed 3D information, the proposed method defuses the unwrapping distortion by controlling the distances between neighboring points. Experimental results will demonstrate the high quality and recognition performance of the 3D unwrapped prints versus traditionally collected 2D prints. Furthermore, by classifying the 3D database into high- and low-quality data sets, we demonstrate that the relationship between quality and recognition performance holding for conventional 2D prints is achieved for 3D unwrapped fingerprints.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-04-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies.

  3. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea.

    PubMed

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50-300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies. PMID:27074710

  4. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea.

    PubMed

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50-300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies.

  5. Observed 3D Structure, Generation, and Dissipation of Oceanic Mesoscale Eddies in the South China Sea

    PubMed Central

    Zhang, Zhiwei; Tian, Jiwei; Qiu, Bo; Zhao, Wei; Chang, Ping; Wu, Dexing; Wan, Xiuquan

    2016-01-01

    Oceanic mesoscale eddies with horizontal scales of 50–300 km are the most energetic form of flows in the ocean. They are the oceanic analogues of atmospheric storms and are effective transporters of heat, nutrients, dissolved carbon, and other biochemical materials in the ocean. Although oceanic eddies have been ubiquitously observed in the world oceans since 1960s, our understanding of their three-dimensional (3D) structure, generation, and dissipation remains fragmentary due to lack of systematic full water-depth measurements. To bridge this knowledge gap, we designed and conducted a multi-months field campaign, called the South China Sea Mesoscale Eddy Experiment (S-MEE), in the northern South China Sea in 2013/2014. The S-MEE for the first time captured full-depth 3D structures of an anticyclonic and cyclonic eddy pair, which are characterized by a distinct vertical tilt of their axes. By observing the eddy evolution at an upstream versus downstream location and conducting an eddy energy budget analysis, the authors further proposed that generation of submesoscale motions most likely constitutes the dominant dissipation mechanism for the observed eddies. PMID:27074710

  6. Application of 3D eddy current analysis on magnetically levitated vehicles

    SciTech Connect

    Fukumoto, H.; Kameoka, Y.; Yoshioka, K.; Takizawa, T.; Kobayashi, T. )

    1993-03-01

    The eddy currents induced on the superconducting magnet (SCM) vessels of magnetically levitated vehicles (MAGLEV) have been analyzed. A 3D eddy current analysis code, based on a finite element method with thin shell approximation, is developed and verified through a mock-up SCM experiment. Through a coupled electromagnetic and mechanical analysis under SCM vibration, a SCM structure with low resistivity material coating on the inner vessel of SCM is found to be suitable for the significant reduction of helium evaporation due to eddy current loss.

  7. On 3-D inelastic analysis methods for hot section components (base program)

    NASA Technical Reports Server (NTRS)

    Wilson, R. B.; Bak, M. J.; Nakazawa, S.; Banerjee, P. K.

    1986-01-01

    A 3-D Inelastic Analysis Method program is described. This program consists of a series of new computer codes embodying a progression of mathematical models (mechanics of materials, special finite element, boundary element) for streamlined analysis of: (1) combustor liners, (2) turbine blades, and (3) turbine vanes. These models address the effects of high temperatures and thermal/mechanical loadings on the local (stress/strain)and global (dynamics, buckling) structural behavior of the three selected components. Three computer codes, referred to as MOMM (Mechanics of Materials Model), MHOST (Marc-Hot Section Technology), and BEST (Boundary Element Stress Technology), have been developed and are briefly described in this report.

  8. Mechanical performance and parameter sensitivity analysis of 3D braided composites joints.

    PubMed

    Wu, Yue; Nan, Bo; Chen, Liang

    2014-01-01

    3D braided composite joints are the important components in CFRP truss, which have significant influence on the reliability and lightweight of structures. To investigate the mechanical performance of 3D braided composite joints, a numerical method based on the microscopic mechanics is put forward, the modeling technologies, including the material constants selection, element type, grid size, and the boundary conditions, are discussed in detail. Secondly, a method for determination of ultimate bearing capacity is established, which can consider the strength failure. Finally, the effect of load parameters, geometric parameters, and process parameters on the ultimate bearing capacity of joints is analyzed by the global sensitivity analysis method. The results show that the main pipe diameter thickness ratio γ, the main pipe diameter D, and the braided angle α are sensitive to the ultimate bearing capacity N.

  9. Mechanical Performance and Parameter Sensitivity Analysis of 3D Braided Composites Joints

    PubMed Central

    Wu, Yue; Nan, Bo; Chen, Liang

    2014-01-01

    3D braided composite joints are the important components in CFRP truss, which have significant influence on the reliability and lightweight of structures. To investigate the mechanical performance of 3D braided composite joints, a numerical method based on the microscopic mechanics is put forward, the modeling technologies, including the material constants selection, element type, grid size, and the boundary conditions, are discussed in detail. Secondly, a method for determination of ultimate bearing capacity is established, which can consider the strength failure. Finally, the effect of load parameters, geometric parameters, and process parameters on the ultimate bearing capacity of joints is analyzed by the global sensitivity analysis method. The results show that the main pipe diameter thickness ratio γ, the main pipe diameter D, and the braided angle α are sensitive to the ultimate bearing capacity N. PMID:25121121

  10. DYNA3D analysis of the DT-20 shipping container

    SciTech Connect

    Logan, R.W.; Lovejoy, S.C.

    1991-08-22

    A DYNA3D model of the DT-20 shipping container was constructed. Impact onto a rigid steel surface at a velocity of 44 ft/sec (30 foot gravity drop) was studied. The orientation of most interest was a side-drop, but end and corner drops were also studied briefly. The assembly for the baseline side impact contained a 150 lb. payload. During this drop, the outer drum sustains plastic strains of up to 0.15, with most the deformation near the rim. The plywood/Celotex packing is crushed about 3 inches. The inner sealed can sees significant stresses, but barely reaches the onset of yielding in some local areas. Based on hand calculations, the bolts joining the can halves could see stresses near 50 ksi. It is felt that overall, the container should survive this drop. However, detailed modeling of the rim closure and the center bolted joint was not possible due to time constraints. Furthermore, better material models and properties are needed for the Celotex, plywood, and honeycomb in particular. 39 figs., 1 tab.

  11. Tensorial analysis of Eshelby stresses in 3D supercooled liquids.

    PubMed

    Lemaître, Anaël

    2015-10-28

    It was recently proposed that the local rearrangements governing relaxation in supercooled liquids impress on the liquid medium long-ranged (Eshelby) stress fluctuations that accumulate over time. From this viewpoint, events must be characterized by elastic dipoles, which are second order tensors, and Eshelby fields are expected to show up in stress and stress increment correlations, which are fourth order tensor fields. We construct here an analytical framework that permits analyzing such tensorial correlations in isotropic media in view of accessing Eshelby fields. Two spherical bases are introduced, which correspond to Cartesian and spherical coordinates for tensors. We show how they can be used to decompose stress correlations and thus test such properties as isotropy and power-law scalings. Eshelby fields and the predicted stress correlations in an infinite medium are shown to belong to an algebra that can conveniently be described using the spherical tensor bases. Using this formalism, we demonstrate that the inherent stress field of 3D supercooled liquids is power law correlated and carries the signature of Eshelby fields, thus supporting the idea that relaxation events give rise to Eshelby stresses that accumulate over time. PMID:26520535

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

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Saunders, J.

    2010-12-01

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

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

    PubMed

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

    2016-04-08

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

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

    NASA Technical Reports Server (NTRS)

    Lietzke, Susan E; Barnes, Cindy L.

    1998-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. Finite Element Analysis of Meniscal Anatomical 3D Scaffolds: Implications for Tissue Engineering

    PubMed Central

    Moroni, L; Lambers, F.M; Wilson, W; van Donkelaar, C.C; de Wijn, JR; Huiskesb, R; van Blitterswijk, C.A

    2007-01-01

    Solid Free-Form Fabrication (SFF) technologies allow the fabrication of anatomical 3D scaffolds from computer tomography (CT) or magnetic resonance imaging (MRI) patients’ dataset. These structures can be designed and fabricated with a variable, interconnected and accessible porous network, resulting in modulable mechanical properties, permeability, and architecture that can be tailored to mimic a specific tissue to replace or regenerate. In this study, we evaluated whether anatomical meniscal 3D scaffolds with matching mechanical properties and architecture are beneficial for meniscus replacement as compared to meniscectomy. After acquiring CT and MRI of porcine menisci, 3D fiber-deposited (3DF) scaffolds were fabricated with different architectures by varying the deposition pattern of the fibers comprising the final structure. The mechanical behaviour of 3DF scaffolds with different architectures and of porcine menisci was measured by static and dynamic mechanical analysis and the effect of these tissue engineering templates on articular cartilage was assessed by finite element analysis (FEA) and compared to healthy conditions or to meniscectomy. Results show that 3DF anatomical menisci scaffolds can be fabricated with pore different architectures and with mechanical properties matching those of natural menisci. FEA predicted a beneficial effect of meniscus replacement with 3D scaffolds in different mechanical loading conditions as compared to meniscectomy. No influence of the internal scaffold architecture was found on articular cartilage damage. Although FEA predictions should be further confirmed by in vitro and in vivo experiments, this study highlights meniscus replacement by SFF anatomical scaffolds as a potential alternative to meniscectomy. PMID:19662124

  17. 2D and 3D reconstruction and geomechanical characterization of kilometre-scale complex folded structures

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  18. Curvilinear Immersed Boundary Method for Simulating Fluid Structure Interaction with Complex 3D Rigid Bodies

    PubMed Central

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2010-01-01

    The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries, Journal of Computational Physics 225 (2007) 1782–1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions unconditionally unstable iteration schemes result even when strong coupling FSI is employed. For such cases, however, combining the strong-coupling iteration with under-relaxation in conjunction with the Aitken’s acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the

  19. Artificial neural networks for 3-D motion analysis-Part II: Nonrigid motion.

    PubMed

    Chen, T; Lin, W C; Chen, C T

    1995-01-01

    For pt. I see ibid., p. 1386-93 (1995). An approach applying artificial neural net techniques to 3D nonrigid motion analysis is proposed. The 3D nonrigid motion of the left ventricle of a human heart is examined using biplanar cineangiography data, consisting of 3D coordinates of 30 coronary artery bifurcation points of the left ventricle and the correspondences of these points taken over 10 time instants during the heart cardiac cycle. The motion is decomposed into global rigid motion and a set of local nonrigid deformations which are coupled with the global motion. The global rigid motion can be estimated precisely as a translation vecto and a rotation matrix. Local nonrigid deformation estimation is discussed. A set of neural nets similar in structure and dynamics but different in physical size is proposed to tackle the problem of nonrigidity. These neural networks are interconnected through feedbacks. The activation function of the output layer is selected so that a feedback is involved in the output updating. The constraints are specified to ensure stable and globally consistent estimation. The objective is to find the optimal deformation matrices that satisfy the constraints for all coronary artery bifurcation points of the left ventricle. The proposed neural networks differ from other existing neural network models in their unique structure and dynamics.

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

    PubMed

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

    2010-09-27

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  2. Tailored complex 3D vortex lattice structures by perturbed multiples of three-plane waves.

    PubMed

    Xavier, Jolly; Vyas, Sunil; Senthilkumaran, Paramasivam; Joseph, Joby

    2012-04-20

    As three-plane waves are the minimum number required for the formation of vortex-embedded lattice structures by plane wave interference, we present our experimental investigation on the formation of complex 3D photonic vortex lattice structures by a designed superposition of multiples of phase-engineered three-plane waves. The unfolding of the generated complex photonic lattice structures with higher order helical phase is realized by perturbing the superposition of a relatively phase-encoded, axially equidistant multiple of three noncoplanar plane waves. Through a programmable spatial light modulator assisted single step fabrication approach, the unfolded 3D vortex lattice structures are experimentally realized, well matched to our computer simulations. The formation of higher order intertwined helices embedded in these 3D spiraling vortex lattice structures by the superposition of the multiples of phase-engineered three-plane waves interference is also studied.

  3. Single cell detection using 3D magnetic rolled-up structures.

    PubMed

    Ger, Tzong-Rong; Huang, Hao-Ting; Huang, Chen-Yu; Lai, Mei-Feng

    2013-11-01

    A 3D rolled-up structure made of a SiO2 layer and a fishbone-like magnetic thin film was proposed here as a biosensor. The magnetoresistance (MR) measurement results of the sensor suggest that the presence of the stray field, which is induced by the magnetic nanoparticles, significantly increased the switching field. Comparing the performance of the 2D sensor and 3D sensor designed in this study, the response in switching field variation was 12.14% in the 2D sensor and 62.55% in the 3D sensor. The response in MR ratio variation was 4.55% in the 2D sensor and 82.32% in the 3D sensor. In addition, the design of the 3D sensor structure also helped to attract and trap a single magnetic cell due to its stronger stray field compared with the 2D structure. The 3D magnetic biosensor designed here can provide important information for future biochip research and applications.

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

    PubMed Central

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

    2015-01-01

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

  5. RETRAN-3D MOD003 Peach Bottom Turbine Trip 2 Multidimensional Kinetics Analysis Models and Results

    SciTech Connect

    Mori, Michitsugu; Ogura, Katsunori; Gose, Garry C.; Wu, J.-Y

    2003-04-15

    An analysis of the Peach Bottom Unit 2 Turbine Trip Test 2 (PB2/TT2) has been performed using RETRAN-3D MOD003. The purpose of the analysis was to investigate the PB2/TT2 overpressurization transient using the RETRAN-3D multidimensional kinetics model.

  6. Three-Axis Distributed Fiber Optic Strain Measurement in 3D Woven Composite Structures

    NASA Technical Reports Server (NTRS)

    Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

    2013-01-01

    Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading. Keywords: fiber optic, distributed strain sensing, Rayleigh scatter, optical frequency domain reflectometry

  7. Three-axis distributed fiber optic strain measurement in 3D woven composite structures

    NASA Astrophysics Data System (ADS)

    Castellucci, Matt; Klute, Sandra; Lally, Evan M.; Froggatt, Mark E.; Lowry, David

    2013-03-01

    Recent advancements in composite materials technologies have broken further from traditional designs and require advanced instrumentation and analysis capabilities. Success or failure is highly dependent on design analysis and manufacturing processes. By monitoring smart structures throughout manufacturing and service life, residual and operational stresses can be assessed and structural integrity maintained. Composite smart structures can be manufactured by integrating fiber optic sensors into existing composite materials processes such as ply layup, filament winding and three-dimensional weaving. In this work optical fiber was integrated into 3D woven composite parts at a commercial woven products manufacturing facility. The fiber was then used to monitor the structures during a VARTM manufacturing process, and subsequent static and dynamic testing. Low cost telecommunications-grade optical fiber acts as the sensor using a high resolution commercial Optical Frequency Domain Reflectometer (OFDR) system providing distributed strain measurement at spatial resolutions as low as 2mm. Strain measurements using the optical fiber sensors are correlated to resistive strain gage measurements during static structural loading.

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

    PubMed Central

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

    2003-01-01

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

  9. 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.

  10. The approximate analysis of the electromagnetic characters of 3-D radome by complex astigmatic wave theory

    NASA Astrophysics Data System (ADS)

    Wang, Yueqing; Wu, Guisheng; Chen, Zhenyang

    The complex astigmatic wave, which imitates the 3-D beam in high-frequency, is an effective method to analyze the electromagnetic characters of the 3-D arbitrarily curved radome. A number of calculations for the ellipsoidal sandwich radome are performed, and the stereoscopic graphics of the results are constructed. Comparing with the experiments, it is shown that this method can be used to simplify analysis and optimization design for many kinds of 3-D radome.

  11. Analysis of wave propagation in periodic 3D waveguides

    NASA Astrophysics Data System (ADS)

    Schaal, Christoph; Bischoff, Stefan; Gaul, Lothar

    2013-11-01

    Structural Health Monitoring (SHM) is a growing research field in the realm of civil engineering. SHM concepts are implemented using integrated sensors and actuators to evaluate the state of a structure. Within this work, wave-based techniques are addressed. Dispersion effects for propagating waves in waveguides of different materials are analyzed for various different cross-sections. Since analytical theory is limited, a general approach based on the Waveguide Finite Element Method is applied. Numerical results are verified experimentally.

  12. 3D building reconstruction from ALS data using unambiguous decomposition into elementary structures

    NASA Astrophysics Data System (ADS)

    Jarząbek-Rychard, M.; Borkowski, A.

    2016-08-01

    The objective of the paper is to develop an automated method that enables for the recognition and semantic interpretation of topological building structures. The novelty of the proposed modeling approach is an unambiguous decomposition of complex objects into predefined simple parametric structures, resulting in the reconstruction of one topological unit without independent overlapping elements. The aim of a data processing chain is to generate complete polyhedral models at LOD2 with an explicit topological structure and semantic information. The algorithms are performed on 3D point clouds acquired by airborne laser scanning. The presented methodology combines data-based information reflected in an attributed roof topology graph with common knowledge about buildings stored in a library of elementary structures. In order to achieve an appropriate balance between reconstruction precision and visualization aspects, the implemented library contains a set of structure-depended soft modeling rules instead of strictly defined geometric primitives. The proposed modeling algorithm starts with roof plane extraction performed by the segmentation of building point clouds, followed by topology identification and recognition of predefined structures. We evaluate the performance of the novel procedure by the analysis of the modeling accuracy and the degree of modeling detail. The assessment according to the validation methods standardized by the International Society for Photogrammetry and Remote Sensing shows that the completeness of the algorithm is above 80%, whereas the correctness exceeds 98%.

  13. 3-D seismic velocity and attenuation structures in the geothermal field

    SciTech Connect

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

    2013-09-09

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  18. 3D printing of weft knitted textile based structures by selective laser sintering of nylon powder

    NASA Astrophysics Data System (ADS)

    Beecroft, M.

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Emmert, Adrian; Kneisel, Christof

    2015-04-01

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

  20. Low-resolution characterization of the 3D structure of the Euglena gracilis photoreceptor

    SciTech Connect

    Barsanti, Laura; Coltelli, Primo; Evangelista, Valtere; Passarelli, Vincenzo; Frassanito, Anna Maria; Vesentini, Nicoletta; Gualtieri, Paolo

    2008-10-24

    This paper deals with the first characterization of the structure of the photoreceptive organelle of the unicellular alga Euglena gracilis (Euglenophyta). This organelle has a three-dimensional organization consisting of up to 50 closely stacked membrane lamellae. Ionically induced unstacking of the photoreceptor lamellae revealed ordered arrays well suited to structural analysis by electron microscopy and image analysis, which ultimately yielded a low-resolution picture of the structure. Each lamella is formed by the photoreceptive membrane protein of the cell assembled within the membrane layer in a hexagonal lattice. The first order diffraction spots in the calculated Fourier transform reveals the presence of 6-fold symmetrized topography (better resolution about 90 A). The 2D and 3D structural data are very similar with those recently published on proteorodopsin, a membrane protein used by marine bacterio-plankton as light-driven proton pump. In our opinion these similarity indicate that a photoreceptive protein belonging to the same superfamily of proteorodopsin could form the Euglena photoreceptor.

  1. 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.

  2. Quasi-3D Waveform Inversion for Velocity Structures and Source Process Analyses Using its Results

    NASA Astrophysics Data System (ADS)

    Hikima, K.; Koketsu, K.

    2007-12-01

    In this study, we propose an efficient waveform inversion method for 2-D velocity structures and 3-D velocity structures are constructed by interpolating the results of the 2-D inversions. We apply these methods to a source process study of the 2003 Miyagi-ken Hokubu earthquake. We will first construct a velocity model, then determine the source processes of this earthquake sequence using the Green's function calculated with the resultant 3-D velocity model. We formulate the inversion procedure in a 2-D cross section. In a 2-D problem, an earthquake is forced to be a line source. Therefore, we introduce approximate transformation from a line source to a point source (Vidale and Helmberger, 1987). We use the 2-D velocity-stress staggered-grid finite difference scheme, so that the source representation is somewhat different from the original 'source box method' and we apply additional corrections to calculated waveforms. The boundary shapes of layers are expressed by connected nodes and we invert observed waveforms for layer thicknesses at the nodes. We perform 2-D velocity inversions along cross sections which involve a medium-size earthquake and observation points. We assemble the results for many stations and interpolated them to construct the 3-D velocity model. Finally, we calculate waveforms from the target earthquake by the 3-D finite difference method with this velocity model to confirm the validity of the model. We next perform waveform inversions for source processes of the 2003 Miyagi-ken Hokubu earthquake sequence using the resultant 3-D velocity model. We divide the fault plane into northern and southern subplanes, so that the southern subplane includes the hypocenter of the mainshock and the largest foreshock. The strike directions of the northern and southern subplanes were N-S and NE-SW, respectively. The Green's functions for these source inversions are calculated using the reciprocal theorem. We determine the slip models using the 3- D structure and

  3. 3D distribution of interstellar medium in the Galaxy: Preparation for analysis of Gaia observations

    SciTech Connect

    Puspitarini, Lucky; Lallement, Rosine

    2015-09-30

    Accurate and detailed three-dimensional (3D) maps of Galactic interstellar medium (ISM) are still lacking. One way to obtain such 3D descriptions is to record a large set of individual absorption or reddening measurements toward target stars located at various known distances and directions. The inversion of these measurements using a tomographic method can produce spatial distribution of the ISM. Until recently absorption data were very limited and distances to the target stars are still uncertain, but the situation will greatly improve thanks to current and future massive stellar surveys from ground, and to Gaia mission. To prepare absorption data for inversion from a huge number of stellar spectra, automated tools are needed. We have developed various spectral analysis tools adapted to different type of spectra, early- or late- type star. We also have used diffuse interstellar bands (DIBs) to trace IS structures and kinematics. Although we do not know yet their carriers, they can be a promising tool to trace distant interstellar clouds or Galactic arms. We present some examples of the interstellar fitting and show the potentiality of DIBs in tracing the ISM. We will also briefly show and comment the latest 3D map of the local ISM which reveal nearby cloud complexes and cavities.

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

    NASA Astrophysics Data System (ADS)

    Kunii, Y.; Sakamoto, R.

    2016-06-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

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

  7. An optical real-time 3D measurement for analysis of facial shape and movement

    NASA Astrophysics Data System (ADS)

    Zhang, Qican; Su, Xianyu; Chen, Wenjing; Cao, Yiping; Xiang, Liqun

    2003-12-01

    Optical non-contact 3-D shape measurement provides a novel and useful tool for analysis of facial shape and movement in presurgical and postsurgical regular check. In this article we present a system, which allows a precise 3-D visualization of the patient's facial before and after craniofacial surgery. We discussed, in this paper, the real time 3-D image capture, processing and the 3-D phase unwrapping method to recover complex shape deformation when the movement of the mouth. The result of real-time measurement for facial shape and movement will be helpful for the more ideal effect in plastic surgery.

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

    PubMed Central

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

    2015-01-01

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

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

    USGS Publications Warehouse

    Safak, E.; Frankel, A.

    1994-01-01

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

  10. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    PubMed

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A

    2009-12-01

    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (http://compbio.cs.princeton.edu/concavity/).

  11. SSME 3-D Turnaround Duct flow analysis - CFD predictions

    NASA Technical Reports Server (NTRS)

    Brankovic, Andreja; Stowers, Steven T.; Mcconnaughey, Paul

    1988-01-01

    CFD analysis is presently employed to obtain an improved flowfield for an individual flowpath in the case of the Space Shuttle Main Engine's High Pressure Fuel Turbopump Turn-Around Duct (TAD), which conducts the flow exiting from the gas turbines into the fuel bowl. It is demonstrated that the application of CFD to TAD flow analysis, giving attention to the duct's configuration and to the number, shape, and alignment of the diffuser struts, can enhance understanding of flow physics and result in improved duct design and performance.

  12. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

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

  13. 3D Printing Meets Computational Astrophysics: Deciphering the Structure of Eta Carinae’s Colliding Winds Using 3D Prints of Smoothed Particle Hydrodynamics Simulations

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  16. 3D multi-layered fibrous cellulose structure using an electrohydrodynamic process for tissue engineering.

    PubMed

    Kim, Minseong; Kim, GeunHyung

    2015-11-01

    Micro/nanofibrous structures have been applied widely in various tissue-engineering applications because the topological structures are similar to the extracellular matrix (ECM), which encourages a high degree of cell adhesion and growth. However, it has been difficult to produce a three-dimensional (3D) fibrous structure using controllable macro-pores. Recently, cellulose has been considered a high-potential natural-origin biomaterial, but its use in 3D biomedical structures has been limited due to its narrow processing window. Here, we suggest a new 3D cellulose scaffold consisting of multi-layered struts made of submicron-sized entangled fibers that were fabricated using an electrohydrodynamic direct jet (EHDJ) process that is spin-printing. By optimizing processing conditions (electric field strength, cellulose feeding rate, and distance between nozzle and target), we can achieve a multi-layered cellulose structure consisting of the cylindrically entangled cellulose fibers. To compare the properties of the fabricated 3D cellulose structure, we used a PCL fibrous scaffold, which has a similar fibrous morphology and pore geometry, as a control. The physical and in vitro biocompatibilities of both fibrous scaffolds were assessed using human dermal fibroblasts, and the cellulose structure showed higher cell adhesion and metabolic activities compared with the control. These results suggest the EHDJ process to be an effective fabricating tool for tissue engineering and the cellulose scaffold has high potential as a tissue regenerative material.

  17. 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

  18. Structure light telecentric stereoscopic vision 3D measurement system based on Scheimpflug condition

    NASA Astrophysics Data System (ADS)

    Mei, Qing; Gao, Jian; Lin, Hui; Chen, Yun; Yunbo, He; Wang, Wei; Zhang, Guanjin; Chen, Xin

    2016-11-01

    We designed a new three-dimensional (3D) measurement system for micro components: a structure light telecentric stereoscopic vision 3D measurement system based on the Scheimpflug condition. This system creatively combines the telecentric imaging model and the Scheimpflug condition on the basis of structure light stereoscopic vision, having benefits of a wide measurement range, high accuracy, fast speed, and low price. The system measurement range is 20 mm×13 mm×6 mm, the lateral resolution is 20 μm, and the practical vertical resolution reaches 2.6 μm, which is close to the theoretical value of 2 μm and well satisfies the 3D measurement needs of micro components such as semiconductor devices, photoelectron elements, and micro-electromechanical systems. In this paper, we first introduce the principle and structure of the system and then present the system calibration and 3D reconstruction. We then present an experiment that was performed for the 3D reconstruction of the surface topography of a wafer, followed by a discussion. Finally, the conclusions are presented.

  19. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  20. Vector algorithms for geometrically nonlinear 3D finite element analysis

    NASA Technical Reports Server (NTRS)

    Whitcomb, John D.

    1989-01-01

    Algorithms for geometrically nonlinear finite element analysis are presented which exploit the vector processing capability of the VPS-32, which is closely related to the CYBER 205. By manipulating vectors (which are long lists of numbers) rather than individual numbers, very high processing speeds are obtained. Long vector lengths are obtained without extensive replication or reordering by storage of intermediate results in strategic patterns at all stages of the computations. Comparisons of execution times with those from programs using either scalar or other vector programming techniques indicate that the algorithms presented are quite efficient.

  1. Multiscale 3D shape analysis using spherical wavelets.

    PubMed

    Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen R

    2005-01-01

    Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data. PMID:16685992

  2. Multiscale 3D Shape Analysis using Spherical Wavelets

    PubMed Central

    Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

    2013-01-01

    Shape priors attempt to represent biological variations within a population. When variations are global, Principal Component Analysis (PCA) can be used to learn major modes of variation, even from a limited training set. However, when significant local variations exist, PCA typically cannot represent such variations from a small training set. To address this issue, we present a novel algorithm that learns shape variations from data at multiple scales and locations using spherical wavelets and spectral graph partitioning. Our results show that when the training set is small, our algorithm significantly improves the approximation of shapes in a testing set over PCA, which tends to oversmooth data. PMID:16685992

  3. 3D inelastic analysis methods for hot section components

    NASA Technical Reports Server (NTRS)

    Dame, L. T.; Chen, P. C.; Hartle, M. S.; Huang, H. T.

    1985-01-01

    The objective is to develop analytical tools capable of economically evaluating the cyclic time dependent plasticity which occurs in hot section engine components in areas of strain concentration resulting from the combination of both mechanical and thermal stresses. Three models were developed. A simple model performs time dependent inelastic analysis using the power law creep equation. The second model is the classical model of Professors Walter Haisler and David Allen of Texas A and M University. The third model is the unified model of Bodner, Partom, et al. All models were customized for linear variation of loads and temperatures with all material properties and constitutive models being temperature dependent.

  4. 3D Kinematics and Hydrodynamic Analysis of Freely Swimming Cetacean

    NASA Astrophysics Data System (ADS)

    Ren, Yan; Sheinberg, Dustin; Liu, Geng; Dong, Haibo; Fish, Frank; Javed, Joveria

    2015-11-01

    It's widely thought that flexibility and the ability to control flexibility are crucial elements in determining the performance of animal swimming. However, there is a lack of quantification of both span-wise and chord-wise deformation of Cetacean's flukes and associated hydrodynamic performance during actively swimming. To fill this gap, we examined the motion and flexure of both dolphin fluke and orca fluke in steady swimming using a combined experimental and computational approach. It is found that the fluke surface morphing can effectively modulate the flow structures and influence the propulsive performance. Findings from this work are fundamental for understanding key kinematic features of effective Cetacean propulsors, and for quantifying the hydrodynamic force production that naturally occurs during different types of swimming. This work is supported by ONR MURI N00014-14-1-0533 and NSF CBET-1313217.

  5. Sub aquatic 3D visualization and temporal analysis utilizing ArcGIS online and 3D applications

    EPA Science Inventory

    We used 3D Visualization tools to illustrate some complex water quality data we’ve been collecting in the Great Lakes. These data include continuous tow data collected from our research vessel the Lake Explorer II, and continuous water quality data collected from an autono...

  6. 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

  7. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    SciTech Connect

    Badger, J. Hendle, J.; Burley, S. K.; Kissinger, C. R.

    2005-09-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

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

    PubMed Central

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

    2016-01-01

    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

  10. 3D flexible NiTi-braided elastomer composites for smart structure applications

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

  11. 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.

  12. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation.

  13. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression

    PubMed Central

    Jacob, J. Augustin; Kumar, N. Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  14. Advanced resin systems and 3D textile preforms for low cost composite structures

    NASA Technical Reports Server (NTRS)

    Shukla, J. G.; Bayha, T. D.

    1993-01-01

    Advanced resin systems and 3D textile preforms are being evaluated at Lockheed Aeronautical Systems Company (LASC) under NASA's Advanced Composites Technology (ACT) Program. This work is aimed towards the development of low-cost, damage-tolerant composite fuselage structures. Resin systems for resin transfer molding and powder epoxy towpreg materials are being evaluated for processability, performance and cost. Three developmental epoxy resin systems for resin transfer molding (RTM) and three resin systems for powder towpregging are being investigated. Various 3D textile preform architectures using advanced weaving and braiding processes are also being evaluated. Trials are being conducted with powdered towpreg, in 2D weaving and 3D braiding processes for their textile processability and their potential for fabrication in 'net shape' fuselage structures. The progress in advanced resin screening and textile preform development is reviewed here.

  15. Structure of complement receptor 2 in complex with its C3d ligand.

    PubMed

    Szakonyi, G; Guthridge, J M; Li, D; Young, K; Holers, V M; Chen, X S

    2001-06-01

    Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design. PMID:11387479

  16. FPGA Implementation of Optimal 3D-Integer DCT Structure for Video Compression.

    PubMed

    Jacob, J Augustin; Kumar, N Senthil

    2015-01-01

    A novel optimal structure for implementing 3D-integer discrete cosine transform (DCT) is presented by analyzing various integer approximation methods. The integer set with reduced mean squared error (MSE) and high coding efficiency are considered for implementation in FPGA. The proposed method proves that the least resources are utilized for the integer set that has shorter bit values. Optimal 3D-integer DCT structure is determined by analyzing the MSE, power dissipation, coding efficiency, and hardware complexity of different integer sets. The experimental results reveal that direct method of computing the 3D-integer DCT using the integer set [10, 9, 6, 2, 3, 1, 1] performs better when compared to other integer sets in terms of resource utilization and power dissipation. PMID:26601120

  17. 3D shape shearography with integrated structured light projection for strain inspection of curved objects

    NASA Astrophysics Data System (ADS)

    Anisimov, Andrei G.; Groves, Roger M.

    2015-05-01

    Shearography (speckle pattern shearing interferometry) is a non-destructive testing technique that provides full-field surface strain characterization. Although real-life objects especially in aerospace, transport or cultural heritage are not flat (e.g. aircraft leading edges or sculptures), their inspection with shearography is of interest for both hidden defect detection and material characterization. Accurate strain measuring of a highly curved or free form surface needs to be performed by combining inline object shape measuring and processing of shearography data in 3D. Previous research has not provided a general solution. This research is devoted to the practical questions of 3D shape shearography system development for surface strain characterization of curved objects. The complete procedure of calibration and data processing of a 3D shape shearography system with integrated structured light projector is presented. This includes an estimation of the actual shear distance and a sensitivity matrix correction within the system field of view. For the experimental part a 3D shape shearography system prototype was developed. It employs three spatially-distributed shearing cameras, with Michelson interferometers acting as the shearing devices, one illumination laser source and a structured light projector. The developed system performance was evaluated with a previously reported cylinder specimen (length 400 mm, external diameter 190 mmm) loaded by internal pressure. Further steps for the 3D shape shearography prototype and the technique development are also proposed.

  18. Parameterization and analysis of 3-D radiative transfer in clouds

    SciTech Connect

    Varnai, Tamas

    2012-03-16

    found that local effects were often much larger than the overall values mentioned above, and were especially large for high sun and near convective clouds such as cumulus. The study also found that statistical methods such as neural networks appear promising for enabling cloud models to consider radiative interactions between nearby atmospheric columns. Finally, through collaboration with German scientists, the project found that new methods (especially one called stepwise kriging) show great promise in filling gaps between cloud radar scans. If applied to data from the new DOE scanning cloud radars, these methods can yield large, continuous three-dimensional cloud structures for future radiative simulations.

  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. 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

  1. Characterizing 3D Structure of Convective Momentum Transport Associated with the MJO Based on Contemporary Reanalyses

    NASA Astrophysics Data System (ADS)

    Oh, J.; Jiang, X.; Waliser, D. E.; Moncrieff, M. W.; Johnson, R. H.

    2013-12-01

    As one of the most prominent tropical atmospheric variability modes, the Madden-Julian Oscillation (MJO) exerts profound influences on global weather and climate, and serves as a critical predictability source for extend-range forecast. While credible representation of the MJO still represents a great challenge for current general circulation models (GCMs), previous studies on the vertical structure of the MJO have largely focused on collective impacts from multi-scale convective systems on thermodynamic properties of the MJO. Most recently, limited observational studies and idealized modeling work suggested that convective momentum transport (CMT) could also play an important role in interpreting the observed MJO features. In this study, the 3D CMT structure associated with the MJO is examined by analyzing model output from three recent high-quality reanalysis systems, including NOAA's Climate Forecast System Reanalysis (CFSR), NASA's Modern Era Retrospective-analysis for Research and Applications (MERRA), and ECMWF-the Year of Tropical Convection (YOTC) reanalysis. Consistent with previous cloud-resolving model study, a well-organized three-layer vertical structure in the CMT associated with the MJO is also discerned based on reanalyses. The result suggests that CMT tends to intensify the MJO circulation, particularly in the lower troposphere. Relative roles of meso-scale systems (MCS) and synoptic waves in contributing the total CMT profiles of the MJO will also be explored. Differences in CMT profiles in these several reanalysis models will be discussed.

  2. 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

  3. 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

  4. Proteopedia: A Collaborative, Virtual 3D Web-Resource for Protein and Biomolecule Structure and Function

    ERIC Educational Resources Information Center

    Hodis, Eran; Prilusky, Jaime, Sussman, Joel L.

    2010-01-01

    Protein structures are hard to represent on paper. They are large, complex, and three-dimensional (3D)--four-dimensional if conformational changes count! Unlike most of their substrates, which can easily be drawn out in full chemical formula, drawing every atom in a protein would usually be a mess. Simplifications like showing only the surface of…

  5. Ion Beam Etching: Replication of Micro Nano-structured 3D Stencil Masks

    SciTech Connect

    Weber, Patrick; Guibert, Edouard; Mikhailov, Serguei; Bruegger, Juergen; Villanueva, Guillermo

    2009-03-10

    Ion beam LIGA allows the etching of 3D nano-structures by direct writing with a nano-sized beam. However, this is a relatively time consuming process. We propose here another approach for etching structures on large surfaces and faster, compared to the direct writing process. This approach consists of replicating 3D structured masks, by scanning an unfocused ion beam. A polymer substrate is placed behind the mask, as in UV photolithography. But the main advantage is that the 3D structure of the mask can be replicated into the polymer. For that purpose, the masks (developped at LMIS1, EPFL) are made of a silicon nitride membrane 100 nm thick, on which 3D gold structures up to 200 nm thick, are deposited. The 3D Au structures are made with the nanostencil method, based on successive gold deposition. The IMA institute, from HE-Arc, owns a High Voltage Engineering 1.7 MV Tandetron with both solid and gaseous negative ion sources, able to generate ions from almost every chemical element in a broad range of energies comprised between 400 keV and 6.8 MeV. The beam composition and energy are chosen in such a way, that ions lose a significant fraction of their energy when passing through the thickest regions of the mask. Ions passing through thinner regions of the mask loose a smaller fraction of their energy and etch the polymer with larger thicknesses, allowing a replication of the mask into the polymer. For our trials, we have used a carbon beam with an energy of 500 keV. The beam was focussed to a diameter of 5 mm with solid slits, in order to avoid border effects and thus ensure a homogeneous dose distribution on the beam diameter. The feasibility of this technique has been demonstrated, allowing industrial applications for micro-mould fabrication, micro-fluidics and micro-optics.

  6. Holographic particle velocimetry - A 3D measurement technique for vortex interactions, coherent structures and turbulence

    NASA Astrophysics Data System (ADS)

    Meng, Hui; Hussain, Fazle

    1991-10-01

    To understand the topology and dynamics of coherent structures (CS), the interactions of CS with fine-scale turbulence, and the effects of CS on entrainment, mixing and combustion, experimental tools are needed that can measure velocity (preferably vorticity) vector fields in both 3D space and time. While traditional measurement techniques are not able to serve this purpose, holographic particle velocimetry (HPV) appears to be promising. In a demonstration experiment, the instantaneous 3D velocity vector fields in some simple vortical flows have been obtained using the HPV technique. In this preliminary report, the principles of the HPV technique are illustrated and the key issues in its implementation are discussed.

  7. Research of aluminium alloy aerospace structure aperture measurement based on 3D digital speckle correlation method

    NASA Astrophysics Data System (ADS)

    Bai, Lu; Wang, Hongbo; Zhou, Jiangfan; Yang, Rong; Zhang, Hui

    2014-11-01

    In this paper, the aperture change of the aluminium alloy aerospace structure under real load is researched. Static experiments are carried on which is simulated the load environment of flight course. Compared with the traditional methods, through experiments results, it's proved that 3D digital speckle correlation method has good adaptability and precision on testing aperture change, and it can satisfy measurement on non-contact,real-time 3D deformation or stress concentration. The test results of new method is compared with the traditional method.

  8. Non-contact 3D fingerprint scanner using structured light illumination

    NASA Astrophysics Data System (ADS)

    Troy, Mike; Hassebrook, Laurence; Yalla, Veeraganesh; Daley, Raymond

    2011-03-01

    As crime prevention and national security remain a top priority, requirements for the use of fingerprints for identification continue to grow. While the size of fingerprint databases continues to expand, new technologies that can improve accuracy and ultimately matching performance will become more critical to maintain the effectiveness of the systems. FlashScan3D has developed non-contact, fingerprint scanners based on the principles of Structured Light Illumination (SLI) that capture 3Dimensional data of fingerprints quickly, accurately and independently of an operator. FlashScan3D will present findings from various research projects performed for the US Army and the Department of Homeland Security.

  9. Studies of the 3D Structure of the Nucleon at JLab

    NASA Astrophysics Data System (ADS)

    Avakian, Harut

    2016-08-01

    Studies of the 3D structure of the nucleon encoded in transverse momentum dependent distribution and fragmentation functions of partons and generalized parton distributions are among the key objectives of the JLab 12 GeV upgrade and the electron ion collider. Main challenges in extracting 3D partonic distributions from precision measurements of hard scattering processes include clear understanding of leading twist QCD fundamentals, higher twist effects, and also correlations of hadron production in target and current fragmentation regions. In this contribution we discuss some ongoing studies and future measurements of spin-orbit correlations at Jefferson Lab.

  10. A Patterned 3D Silicon Anode Fabricated by Electrodeposition on a Virus-Structured Current Collector

    SciTech Connect

    Chen, X L; Gerasopoulos, K; Guo, J C; Brown, A; Wang, Chunsheng; Ghodssi, Reza; Culver, J N

    2010-11-09

    Electrochemical methods were developed for the deposition of nanosilicon onto a 3D virus-structured nickel current collector. This nickel current collector is composed of self-assembled nanowire-like rods of genetically modified tobacco mosaic virus (TMV1cys), chemically coated in nickel to create a complex high surface area conductive substrate. The electrochemically depo­sited 3D silicon anodes demonstrate outstanding rate performance, cycling stability, and rate capability. Electrodeposition thus provides a unique means of fabricating silicon anode materials on complex substrates at low cost.

  11. Prediction of spin-dependent electronic structure in 3d-transition-metal doped antimonene

    NASA Astrophysics Data System (ADS)

    Yang, L. F.; Song, Y.; Mi, W. B.; Wang, X. C.

    2016-07-01

    We investigate the geometric structure and electronic and magnetic properties of 3d-transition-metal atom doped antimonene using spin-polarized first-principles calculations. Strong orbital hybridization exhibits between 3d-transition-metal and Sb atoms, where covalent bonds form in antimonene. A spin-polarized semiconducting state appears in Cr-doped antimonene, while half-metallic states appear by doping Ti, V, and Mn. These findings indicate that once combined with doping states, the bands of antimonene systems offer a variety of features. Specific dopants lead to half-metallic characters with high spin polarization that has potential application in spintronics.

  12. Parameterization and Analysis of 3-D Solar Radiative Transfer in Clouds: Final Report

    SciTech Connect

    Jerry Y. Harrington

    2012-09-21

    This document reports on the research that we have done over the course of our two-year project. The report also covers the research done on this project during a 1 year no-cost extension of the grant. Our work has had two main, inter-related thrusts: The first thrust was to characterize the response of stratocumulus cloud structure and dynamics to systematic changes in cloud infrared radiative cooling and solar heating using one-dimensional radiative transfer models. The second was to couple a three-dimensional (3-D) solar radiative transfer model to the Large Eddy Simulation (LES) model that we use to simulate stratocumulus. The purpose of the studies with 3-D radiative transfer was to examine the possible influences of 3-D photon transport on the structure, evolution, and radiative properties of stratocumulus. While 3-D radiative transport has been examined in static cloud environments, few studies have attempted to examine whether the 3-D nature of radiative absorption and emission influence the structure and evolution of stratocumulus. We undertook this dual approach because only a small number of LES simulations with the 3-D radiative transfer model are possible due to the high computational costs. Consequently, LES simulations with a 1-D radiative transfer solver were used in order to examine the portions of stratocumulus parameter space that may be most sensitive to perturbations in the radiative fields. The goal was then to explore these sensitive regions with LES using full 3-D radiative transfer. Our overall goal was to discover whether 3-D radiative processes alter cloud structure and evolution, and whether this may have any indirect implications for cloud radiative properties. In addition, we collaborated with Dr. Tamas Varni, providing model output fields for his attempt at parameterizing 3-D radiative effects for cloud models.

  13. JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

    PubMed

    Ribes, Delphine; Parafita, Julia; Charrier, Rémi; Magara, Fulvio; Magistretti, Pierre J; Thiran, Jean-Philippe

    2010-11-23

    In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

  14. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  15. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  16. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-08-09

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

  17. Analysis of the Possibilities of Using Low-Cost Scanning System in 3d Modeling

    NASA Astrophysics Data System (ADS)

    Kedzierski, M.; Wierzbickia, D.; Fryskowska, A.; Chlebowska, B.

    2016-06-01

    The laser scanning technique is still a very popular and fast growing method of obtaining information on modeling 3D objects. The use of low-cost miniature scanners creates new opportunities for small objects of 3D modeling based on point clouds acquired from the scan. The same, the development of accuracy and methods of automatic processing of this data type is noticeable. The article presents methods of collecting raw datasets in the form of a point-cloud using a low-cost ground-based laser scanner FabScan. As part of the research work 3D scanner from an open source FabLab project was constructed. In addition, the results for the analysis of the geometry of the point clouds obtained by using a low-cost laser scanner were presented. Also, some analysis of collecting data of different structures (made of various materials such as: glass, wood, paper, gum, plastic, plaster, ceramics, stoneware clay etc. and of different shapes: oval and similar to oval and prism shaped) have been done. The article presents two methods used for analysis: the first one - visual (general comparison between the 3D model and the real object) and the second one - comparative method (comparison between measurements on models and scanned objects using the mean error of a single sample of observations). The analysis showed, that the low-budget ground-based laser scanner FabScan has difficulties with collecting data of non-oval objects. Items built of glass painted black also caused problems for the scanner. In addition, the more details scanned object contains, the lower the accuracy of the collected point-cloud is. Nevertheless, the accuracy of collected data (using oval-straight shaped objects) is satisfactory. The accuracy, in this case, fluctuates between ± 0,4 mm and ± 1,0 mm whereas when using more detailed objects or a rectangular shaped prism the accuracy is much more lower, between 2,9 mm and ± 9,0 mm. Finally, the publication presents the possibility (for the future expansion of

  18. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  19. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-11-25

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  20. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    NASA Astrophysics Data System (ADS)

    Zenou, M.; Sa'Ar, A.; Kotler, Z.

    2015-11-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures.

  1. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

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

    PubMed

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

    2016-06-01

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

  3. Influence of 3D anisotropic structures on bipole-quadrupole DC resistivity (BQ-DC) measurements

    NASA Astrophysics Data System (ADS)

    Loewer, A.; Junge, A.; Guenther, T.; Grinat, M.; Hering, P.

    2015-12-01

    3D modelling of BQ-DC measurements can show a rather strong directional distortion of the electric current density for an inhomogeneous subsurface. Anisotropic structures increase this effect. Depending on the anisotropy direction, current density might vary by 90° between the interior and exterior of an anisotropic body. In combination with 3D effects currents might even flow into the opposite direction compared to those expected for a homogeneous half space. This effect can produce negative potential differences (in combination with positive geometry factors) at the surface which cannot be explained by an isotropic resistivity distribution and thus those data cannot be used by an isotropic inversion. Consequently, anisotropic forward modelling is necessary to explain such observations. In nature anisotropic resistivity can appear in the context of strongly foliated structures. Such structures exist in the Rhenish Massif, Germany, where extensive shallow greywacke shales with different strength of foliation are found. In this area a field campaign was performed in 2014 to provide evidence for the existence of anisotropic resistivity structures. Two perpendicular bipole current injections at 15 locations produced individual potential distributions. The potential differences were recorded for two orthogonal directions each at 30 positions for an array set up within the survey area. We use the apparent resistivity tensor after Bibby 1986 to display the BQ-DC data. It uses the hypothetical current densities of each of the two bipole sources calculated for an equivalent homogenous half space at the location of the quadrupole measurement to derive a resistivity tensor. The spatial behavior of modelled tensors gives evidence of the anisotropic body although the structure is covered by an isotropic layer. The data are explained by a 3D anisotropic resistivity distribution using a 3D isotropic inversion scheme combined with 3D anisotropic forward-modelling.

  4. EK3D: an E. coli K antigen 3-dimensional structure database

    PubMed Central

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host–pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  5. Fabrication of 3D microfluidic structures inside glass by femtosecond laser micromachining

    NASA Astrophysics Data System (ADS)

    Sugioka, Koji; Cheng, Ya

    2014-01-01

    Femtosecond lasers have opened up new avenues in materials processing due to their unique characteristics of ultrashort pulse widths and extremely high peak intensities. One of the most important features of femtosecond laser processing is that a femtosecond laser beam can induce strong absorption in even transparent materials due to nonlinear multiphoton absorption. This makes it possible to directly create three-dimensional (3D) microfluidic structures in glass that are of great use for fabrication of biochips. For fabrication of the 3D microfluidic structures, two technical approaches are being attempted. One of them employs femtosecond laser-induced internal modification of glass followed by wet chemical etching using an acid solution (Femtosecond laser-assisted wet chemical etching), while the other one performs femtosecond laser 3D ablation of the glass in distilled water (liquid-assisted femtosecond laser drilling). This paper provides a review on these two techniques for fabrication of 3D micro and nanofluidic structures in glass based on our development and experimental results.

  6. EK3D: an E. coli K antigen 3-dimensional structure database.

    PubMed

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host-pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  7. Structuring Narrative in 3D Digital Game-Based Learning Environments to Support Second Language Acquisition

    ERIC Educational Resources Information Center

    Neville, David O.

    2010-01-01

    The essay is a conceptual analysis from an instructional design perspective exploring the feasibility of using three-dimensional digital game-based learning (3D-DGBL) environments to assist in second language acquisition (SLA). It examines the shared characteristics of narrative within theories of situated cognition, context-based approaches to…

  8. In-chip fabrication of free-form 3D constructs for directed cell migration analysis.

    PubMed

    Olsen, Mark Holm; Hjortø, Gertrud Malene; Hansen, Morten; Met, Özcan; Svane, Inge Marie; Larsen, Niels B

    2013-12-21

    Free-form constructs with three-dimensional (3D) microporosity were fabricated by two-photon polymerization inside the closed microchannel of an injection-molded, commercially available polymer chip for analysis of directed cell migration. Acrylate constructs were produced as woodpile topologies with a range of pore sizes from 5 × 5 μm to 15 × 15 μm and prefilled with fibrillar collagen. Dendritic cells seeded into the polymer chip in a concentration gradient of the chemoattractant CCL21 efficiently negotiated the microporous maze structure for pore sizes of 8 × 8 μm or larger. The cells migrating through smaller pore sizes made significantly more turns than those through larger pores. The introduction of additional defined barriers in the microporous structure resulted in dendritic cells making more turns while still being able to follow the chemoattractant concentration gradient.

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

    PubMed

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

    2015-07-01

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

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

    PubMed

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

    2015-07-01

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

  11. The theoretical 3D structure of Bacillus thuringiensis Cry5Ba.

    PubMed

    Xia, Li-Qiu; Zhao, Xin-Min; Ding, Xue-Zhi; Wang, Fa-Xiang; Sun, Yun-Jun

    2008-09-01

    Cry5Ba is a delta-endotoxin produced by Bacillus thuringiensis PS86A1 NRRL B-18900. It is active against nematodes and has great potential for nematode control. Here, we predict the first theoretical model of the three-dimensional (3D) structure of a Cry5Ba toxin by homology modeling on the structure of the Cry1Aa toxin, which is specific to Lepidopteran insects. Cry5Ba resembles the previously reported Cry1Aa toxin structure in that they share a common 3D structure with three domains, but there are some distinctions, with the main differences being located in the loops of domain I. Cry5Ba exhibits a changeable extending conformation structure, and this special structure may also be involved in pore-forming and specificity determination. A fuller understanding of the 3D structure will be helpful in the design of mutagenesis experiments aimed at improving toxicity, and lead to a deep understanding of the mechanism of action of nematicidal toxins.

  12. 3D finite element model of the diabetic neuropathic foot: a gait analysis driven approach.

    PubMed

    Guiotto, Annamaria; Sawacha, Zimi; Guarneri, Gabriella; Avogaro, Angelo; Cobelli, Claudio

    2014-09-22

    Diabetic foot is an invalidating complication of diabetes that can lead to foot ulcers. Three-dimensional (3D) finite element analysis (FEA) allows characterizing the loads developed in the different anatomical structures of the foot in dynamic conditions. The aim of this study was to develop a subject specific 3D foot FE model (FEM) of a diabetic neuropathic (DNS) and a healthy (HS) subject, whose subject specificity can be found in term of foot geometry and boundary conditions. Kinematics, kinetics and plantar pressure (PP) data were extracted from the gait analysis trials of the two subjects with this purpose. The FEM were developed segmenting bones, cartilage and skin from MRI and drawing a horizontal plate as ground support. Materials properties were adopted from previous literature. FE simulations were run with the kinematics and kinetics data of four different phases of the stance phase of gait (heel strike, loading response, midstance and push off). FEMs were then driven by group gait data of 10 neuropathic and 10 healthy subjects. Model validation focused on agreement between FEM-simulated and experimental PP. The peak values and the total distribution of the pressures were compared for this purpose. Results showed that the models were less robust when driven from group data and underestimated the PP in each foot subarea. In particular in the case of the neuropathic subject's model the mean errors between experimental and simulated data were around the 20% of the peak values. This knowledge is crucial in understanding the aetiology of diabetic foot.

  13. A 3D endoscopy reconstruction as a saliency map for analysis of polyp shapes

    NASA Astrophysics Data System (ADS)

    Ruano, Josue; Martínez, Fabio; Gómez, Martín.; Romero, Eduardo

    2015-01-01

    A first diagnosis of colorectal cancer is performed by examination of polyp shape and appearance during an endoscopy routine procedure. However, the video-endoscopy is highly noisy because exacerbated physiological conditions like increased motility or secretion may limit the visual analysis of lesions. In this work a 3D reconstruction of the digestive tract is proposed, facilitating the polyp shape evaluation by highlighting its surface geometry and allowing an analysis from different perspectives. The method starts by a spatio-temporal map, constructed to group the different regions of the tract by their similar dynamic patterns during the sequence. Then, such map was convolved with a second derivative of a Gaussian kernel that emulates the camera distortion and allows to highlight the polyp surface. The position initialization in each frame of the kernel was computed from expert manual delineation and propagated along the sequence based on. Results show reliable reconstructions, with a salient 3D polyp structure that can then be better observed.

  14. Parametric estimation of 3D tubular structures for diffuse optical tomography

    PubMed Central

    Larusson, Fridrik; Anderson, Pamela G.; Rosenberg, Elizabeth; Kilmer, Misha E.; Sassaroli, Angelo; Fantini, Sergio; Miller, Eric L.

    2013-01-01

    We explore the use of diffuse optical tomography (DOT) for the recovery of 3D tubular shapes representing vascular structures in breast tissue. Using a parametric level set method (PaLS) our method incorporates the connectedness of vascular structures in breast tissue to reconstruct shape and absorption values from severely limited data sets. The approach is based on a decomposition of the unknown structure into a series of two dimensional slices. Using a simplified physical model that ignores 3D effects of the complete structure, we develop a novel inter-slice regularization strategy to obtain global regularity. We report on simulated and experimental reconstructions using realistic optical contrasts where our method provides a more accurate estimate compared to an unregularized approach and a pixel based reconstruction. PMID:23411913

  15. Finite Element Analysis of Mechanical Properties of 3D Four-directional Rectangular Braided Composites—Part 2: Validation of the 3D Finite Element Model

    NASA Astrophysics Data System (ADS)

    Li, Dian-Sen; Fang, Dai-Ning; Lu, Zi-Xing; Yang, Zhen-Yu; Jiang, Nan

    2010-08-01

    In the first part of the work, we have established a new parameterized three-dimensional (3D) finite element model (FEM) which precisely simulated the spatial configuration of the braiding yarns and considered the cross-section deformation as well as the surface contact relationship between the yarns. This paper presents a prediction of the effective elastic properties and the meso-scale mechanical response of 3D braided composites to verify the validation of the FEM. The effects of the braiding parameters on the mechanical properties are investigated in detail. By analyzing the deformation and stress nephogram of the model, a reasonable overall stress field is provided and the results well support the strength prediction. The results indicate it is convenient to predict all the elastic constants of 3D braided composites with different parameters simultaneously using the FEM. Moreover, the FEM can successfully predict the meso-scale mechanical response of 3D braided composites containing periodical structures.

  16. RESTRUCTURING RELAP5-3D FOR NEXT GENERATION NUCLEAR PLANT ANALYSIS

    SciTech Connect

    Donna Post Guillen; George L. Mesina; Joshua M. Hykes

    2006-06-01

    RELAP5-3D is used worldwide for analyzing nuclear reactors under both operational transients and postulated accident conditions. Development of the RELAP code series began in 1975 and since that time the code has been continuously improved, enhanced, verified and validated [1]. Since RELAP5-3D will continue to be the premier thermal hydraulics tool well into the future, it is necessary to modernize the code to accommodate the incorporation of additional capabilities to support the development of the next generation of nuclear reactors [2]. This paper discusses the reengineering of RELAP5-3D into structured code.

  17. The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays

    PubMed Central

    Dubrovin, E. V.; Presnova, G. V.; Rubtsova, M. Yu.; Egorov, A. M.; Grigorenko, V. G.; Yaminsky, I. V.

    2015-01-01

    Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles. PMID:26085952

  18. 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.

  19. Image enhancement and segmentation of fluid-filled structures in 3D ultrasound images

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Dudycha, Stephen; McMorrow, Gerald

    2003-05-01

    Segmentation of fluid-filled structures, such as the urinary bladder, from three-dimensional ultrasound images is necessary for measuring their volume. This paper describes a system for image enhancement, segmentation and volume measurement of fluid-filled structures on 3D ultrasound images. The system was applied for the measurement of urinary bladder volume. Results show an average error of less than 10% in the estimation of the total bladder volume.

  20. Optical fibre sensing in metals by embedment in 3D printed metallic structures

    NASA Astrophysics Data System (ADS)

    Maier, R. R. J.; Havermann, D.; Schneller, O.; Mathew, J.; Polyzos, D.; MacPherson, W. N.; Hand, D. P.

    2014-05-01

    Additive manufacturing or 3D printing of structural components in metals has potential to revolutionise the manufacturing industry. Embedded sensing in such structures opens a route towards SMART metals, providing added functionality, intelligence and enhanced performance in many components. Such embedded sensors would be capable of operating at extremely high temperatures by utilizing regenerated fibre Bragg gratings and in-fibre Fabry-Perot cavities.

  1. ModeRNA: a tool for comparative modeling of RNA 3D structure

    PubMed Central

    Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

    2011-01-01

    RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

  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. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications. PMID:25982877

  4. Factors Affecting Dimensional Accuracy of 3-D Printed Anatomical Structures Derived from CT Data.

    PubMed

    Ogden, Kent M; Aslan, Can; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Soman, Pranav

    2015-12-01

    Additive manufacturing and bio-printing, with the potential for direct fabrication of complex patient-specific anatomies derived from medical scan data, are having an ever-increasing impact on the practice of medicine. Anatomic structures are typically derived from CT or MRI scans, and there are multiple steps in the model derivation process that influence the geometric accuracy of the printed constructs. In this work, we compare the dimensional accuracy of 3-D printed constructs of an L1 vertebra derived from CT data for an ex vivo cadaver T-L spine with the original vertebra. Processing of segmented structures using binary median filters and various surface extraction algorithms is evaluated for the effect on model dimensions. We investigate the effects of changing CT reconstruction kernels by scanning simple geometric objects and measuring the impact on the derived model dimensions. We also investigate if there are significant differences between physical and virtual model measurements. The 3-D models were printed using a commercial 3-D printer, the Replicator 2 (MakerBot, Brooklyn, NY) using polylactic acid (PLA) filament. We found that changing parameters during the scan reconstruction, segmentation, filtering, and surface extraction steps will have an effect on the dimensions of the final model. These effects need to be quantified for specific situations that rely on the accuracy of 3-D printed models used in medicine or tissue engineering applications.

  5. Generation of 3-D surface maps in waste storage silos using a structured light source

    NASA Technical Reports Server (NTRS)

    Burks, B. L.; Rowe, J. C.; Dinkins, M. A.; Christensen, B.; Selleck, C.; Jacoboski, D.; Markus, R.

    1992-01-01

    Surface contours inside the large waste storage tanks typical of the Department of Energy (DOE) complex are, in general, highly irregular. In addition to pipes and other pieces of equipment in the tanks, the surfaces may have features such as mounds, fissures, crystalline structures, and mixed solid and liquid forms. Prior to remediation activities, it will be necessary to characterize the waste to determine the most effective remediation approaches. Surface contour data will be required both prior to and during remediation. The use is described of a structured light source to generate 3-D surface contour maps of the interior of waste storage silos at the Feed Materials Production Center at Fernald, OH. The landscape inside these large waste storage tanks bears a strong resemblance to some of the landscapes that might be encountered during lunar or planetary exploration. Hence, these terrestrial 3-D mapping techniques may be directly applicable to extraterrestrial exploration. In further development, it will be demonstrated that these 3-D data can be used for robotic task planning just as 3-D surface contour data of a satellite could be used to plan maintenance tasks for a space-based servicing robot.

  6. Structured Light Based 3d Scanning for Specular Surface by the Combination of Gray Code and Phase Shifting

    NASA Astrophysics Data System (ADS)

    Zhang, Yujia; Yilmaz, Alper

    2016-06-01

    Surface reconstruction using coded structured light is considered one of the most reliable techniques for high-quality 3D scanning. With a calibrated projector-camera stereo system, a light pattern is projected onto the scene and imaged by the camera. Correspondences between projected and recovered patterns are computed in the decoding process, which is used to generate 3D point cloud of the surface. However, the indirect illumination effects on the surface, such as subsurface scattering and interreflections, will raise the difficulties in reconstruction. In this paper, we apply maximum min-SW gray code to reduce the indirect illumination effects of the specular surface. We also analysis the errors when comparing the maximum min-SW gray code and the conventional gray code, which justifies that the maximum min-SW gray code has significant superiority to reduce the indirect illumination effects. To achieve sub-pixel accuracy, we project high frequency sinusoidal patterns onto the scene simultaneously. But for specular surface, the high frequency patterns are susceptible to decoding errors. Incorrect decoding of high frequency patterns will result in a loss of depth resolution. Our method to resolve this problem is combining the low frequency maximum min-SW gray code and the high frequency phase shifting code, which achieves dense 3D reconstruction for specular surface. Our contributions include: (i) A complete setup of the structured light based 3D scanning system; (ii) A novel combination technique of the maximum min-SW gray code and phase shifting code. First, phase shifting decoding with sub-pixel accuracy. Then, the maximum min-SW gray code is used to resolve the ambiguity resolution. According to the experimental results and data analysis, our structured light based 3D scanning system enables high quality dense reconstruction of scenes with a small number of images. Qualitative and quantitative comparisons are performed to extract the advantages of our new

  7. The degree of π electron delocalization and the formation of 3D-extensible sandwich structures.

    PubMed

    Wang, Xiang; Wang, Qiang; Yuan, Caixia; Zhao, Xue-Feng; Li, Jia-Jia; Li, Debao; Wu, Yan-Bo; Wang, Xiaotai

    2016-04-28

    DFT B3LYP/6-31G(d) calculations were performed to examine the feasibility of graphene-like C42H18 and starbenzene C6(BeH)6 (SBz) polymers as ligands of 3D-extensible sandwich compounds (3D-ESCs) with uninterrupted sandwich arrays. The results revealed that sandwich compounds with three or more C42H18 ligands were not feasible. The possible reason may be the localization of π electrons on certain C6 hexagons due to π-metal interactions, which makes the whole ligand lose its electronic structure basis (higher degree of π electron delocalization) to maintain the planar structure. For comparison, with the aid of benzene (Bz) molecules, the SBz polymers can be feasible ligands for designing 3D-ESCs because the C-Be interactions in individual SBz are largely ionic, which will deter the π electrons on one C6 ring from connecting to those on neighbouring C6 rings. This means that high degree of π electron delocalization is not necessary for maintaining the planarity of SBz polymers. Such a locally delocalized π electron structure is desirable for the ligands of 3D-ESCs. Remarkably, the formation of a sandwich compound with SBz is thermodynamically more favourable than that found for bis(Bz)chromium. The assembly of 3D-ESCs is largely exothermic, which will facilitate future experimental synthesis. The different variation trends on the HOMO-LUMO gaps in different directions (relative to the sandwich axes) suggest that they can be developed to form directional conductors or semiconductors, which may be useful in the production of electronic devices. PMID:27004750

  8. Optimal Image Stitching for Concrete Bridge Bottom Surfaces Aided by 3d Structure Lines

    NASA Astrophysics Data System (ADS)

    Liu, Yahui; Yao, Jian; Liu, Kang; Lu, Xiaohu; Xia, Menghan

    2016-06-01

    Crack detection for bridge bottom surfaces via remote sensing techniques is undergoing a revolution in the last few years. For such applications, a large amount of images, acquired with high-resolution industrial cameras close to the bottom surfaces with some mobile platform, are required to be stitched into a wide-view single composite image. The conventional idea of stitching a panorama with the affine model or the homographic model always suffers a series of serious problems due to poor texture and out-of-focus blurring introduced by depth of field. In this paper, we present a novel method to seamlessly stitch these images aided by 3D structure lines of bridge bottom surfaces, which are extracted from 3D camera data. First, we propose to initially align each image in geometry based on its rough position and orientation acquired with both a laser range finder (LRF) and a high-precision incremental encoder, and these images are divided into several groups with the rough position and orientation data. Secondly, the 3D structure lines of bridge bottom surfaces are extracted from the 3D cloud points acquired with 3D cameras, which impose additional strong constraints on geometrical alignment of structure lines in adjacent images to perform a position and orientation optimization in each group to increase the local consistency. Thirdly, a homographic refinement between groups is applied to increase the global consistency. Finally, we apply a multi-band blending algorithm to generate a large-view single composite image as seamlessly as possible, which greatly eliminates both the luminance differences and the color deviations between images and further conceals image parallax. Experimental results on a set of representative images acquired from real bridge bottom surfaces illustrate the superiority of our proposed approaches.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  10. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure

    NASA Astrophysics Data System (ADS)

    Prilusky, Jaime; Hodis, Eran; Sussman, Joel L.

    Proteopedia is a collaborative, 3D web-encyclopedia of protein, nucleic acid and other structures. Proteopedia ( http://www.proteopedia.org ) presents 3D biomolecule structures in a broadly accessible manner to a diverse scientific audience through easy-to-use molecular visualization tools integrated into a wiki environment that anyone with a user account can edit. We describe recent advances in the web resource in the areas of content and software. In terms of content, we describe a large growth in user-added content as well as improvements in automatically-generated content for all PDB entry pages in the resource. In terms of software, we describe new features ranging from the capability to create pages hidden from public view to the capability to export pages for offline viewing. New software features also include an improved file-handling system and availability of biological assemblies of protein structures alongside their asymmetric units.

  11. A 3D-Video-Based Computerized Analysis of Social and Sexual Interactions in Rats

    PubMed Central

    Matsumoto, Jumpei; Urakawa, Susumu; Takamura, Yusaku; Malcher-Lopes, Renato; Hori, Etsuro; Tomaz, Carlos; Ono, Taketoshi; Nishijo, Hisao

    2013-01-01

    A large number of studies have analyzed social and sexual interactions between rodents in relation to neural activity. Computerized video analysis has been successfully used to detect numerous behaviors quickly and objectively; however, to date only 2D video recording has been used, which cannot determine the 3D locations of animals and encounters difficulties in tracking animals when they are overlapping, e.g., when mounting. To overcome these limitations, we developed a novel 3D video analysis system for examining social and sexual interactions in rats. A 3D image was reconstructed by integrating images captured by multiple depth cameras at different viewpoints. The 3D positions of body parts of the rats were then estimated by fitting skeleton models of the rats to the 3D images using a physics-based fitting algorithm, and various behaviors were recognized based on the spatio-temporal patterns of the 3D movements of the body parts. Comparisons between the data collected by the 3D system and those by visual inspection indicated that this system could precisely estimate the 3D positions of body parts for 2 rats during social and sexual interactions with few manual interventions, and could compute the traces of the 2 animals even during mounting. We then analyzed the effects of AM-251 (a cannabinoid CB1 receptor antagonist) on male rat sexual behavior, and found that AM-251 decreased movements and trunk height before sexual behavior, but increased the duration of head-head contact during sexual behavior. These results demonstrate that the use of this 3D system in behavioral studies could open the door to new approaches for investigating the neuroscience of social and sexual behavior. PMID:24205238

  12. A 3D-video-based computerized analysis of social and sexual interactions in rats.

    PubMed

    Matsumoto, Jumpei; Urakawa, Susumu; Takamura, Yusaku; Malcher-Lopes, Renato; Hori, Etsuro; Tomaz, Carlos; Ono, Taketoshi; Nishijo, Hisao

    2013-01-01

    A large number of studies have analyzed social and sexual interactions between rodents in relation to neural activity. Computerized video analysis has been successfully used to detect numerous behaviors quickly and objectively; however, to date only 2D video recording has been used, which cannot determine the 3D locations of animals and encounters difficulties in tracking animals when they are overlapping, e.g., when mounting. To overcome these limitations, we developed a novel 3D video analysis system for examining social and sexual interactions in rats. A 3D image was reconstructed by integrating images captured by multiple depth cameras at different viewpoints. The 3D positions of body parts of the rats were then estimated by fitting skeleton models of the rats to the 3D images using a physics-based fitting algorithm, and various behaviors were recognized based on the spatio-temporal patterns of the 3D movements of the body parts. Comparisons between the data collected by the 3D system and those by visual inspection indicated that this system could precisely estimate the 3D positions of body parts for 2 rats during social and sexual interactions with few manual interventions, and could compute the traces of the 2 animals even during mounting. We then analyzed the effects of AM-251 (a cannabinoid CB1 receptor antagonist) on male rat sexual behavior, and found that AM-251 decreased movements and trunk height before sexual behavior, but increased the duration of head-head contact during sexual behavior. These results demonstrate that the use of this 3D system in behavioral studies could open the door to new approaches for investigating the neuroscience of social and sexual behavior. PMID:24205238

  13. Mobile 3D quality of experience evaluation: a hybrid data collection and analysis approach

    NASA Astrophysics Data System (ADS)

    Utriainen, Timo; Häyrynen, Jyrki; Jumisko-Pyykkö, Satu; Boev, Atanas; Gotchev, Atanas; Hannuksela, Miska M.

    2011-02-01

    The paper presents a hybrid approach to study the user's experienced quality of 3D visual content on mobile autostereoscopic displays. It combines extensive subjective tests with collection and objective analysis of eye-tracked data. 3D cues which are significant for mobiles are simulated in the generated 3D test content. The methodology for conducting subjective quality evaluation includes hybrid data-collection of quantitative quality preferences, qualitative impressions, and binocular eye-tracking. We present early results of the subjective tests along with eye movement reaction times, areas of interest and heatmaps obtained from raw eye-tracked data after statistical analysis. The study contributes to the question what is important to be visualized on portable auto-stereoscopic displays and how to maintain and visually enhance the quality of 3D content for such displays.

  14. Topological evolutionary computing in the optimal design of 2D and 3D structures

    NASA Astrophysics Data System (ADS)

    Burczynski, T.; Poteralski, A.; Szczepanik, M.

    2007-10-01

    An application of evolutionary algorithms and the finite-element method to the topology optimization of 2D structures (plane stress, bending plates, and shells) and 3D structures is described. The basis of the topological evolutionary optimization is the direct control of the density material distribution (or thickness for 2D structures) by the evolutionary algorithm. The structures are optimized for stress, mass, and compliance criteria. The numerical examples demonstrate that this method is an effective technique for solving problems in computer-aided optimal design.

  15. Analysis of the KROTOS KFC test by coupling X-Ray image analysis and MC3D calculations

    SciTech Connect

    Brayer, C.; Charton, A.; Grishchenko, D.; Fouquart, P.; Bullado, Y.; Compagnon, F.; Correggio, P.; Cassiaut-Louis, N.; Piluso, P.

    2012-07-01

    During a hypothetical severe accident sequence in a Pressurized Water Reactor (PWR), the hot molten materials (corium) issuing from the degraded reactor core may generate a steam explosion if they come in contact with water and may damage the structures and threaten the reactor integrity. The SERENA program is an international OECD project that aims at helping the understanding of this phenomenon also called Fuel Coolant Interaction (FCI) by providing data. CEA takes part in this program by performing tests in its KROTOS facility where steam explosions using prototypic corium can be triggered. Data about the different phases in the premixing are extracted from the KROTOS X-Ray radioscopy images by using KIWI software (KROTOS Image analysis of Water-corium Interaction) currently developed by CEA. The MC3D code, developed by IRSN, is a thermal-hydraulic multiphase code mainly dedicated to FCI studies. It is composed of two applications: premixing and explosion. An overall FCI calculation with MC3D requires a premixing calculation followed by an explosion calculation. The present paper proposes an alternative approach in which all the features of the premixing are extracted from the X-Ray pictures using the KIWI software and transferred to an MC3D dataset for a direct simulation of the explosion. The main hypothesis are discussed as well as the first explosion results obtained with MC3D for the KROTOS KFC test. These results are rather encouraging and are analyzed on the basis of comparisons with the experimental data. (authors)

  16. 3D structure and conductive thermal field of the Upper Rhine Graben

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  17. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases. PMID:26231917

  18. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  19. Potential energy curves and electronic structure of 3d transition metal hydrides and their cations

    NASA Astrophysics Data System (ADS)

    Goel, Satyender; Masunov, Artëm E.

    2008-12-01

    We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese-Martin for kinetics (BMK) and Tao-Perdew-Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree-Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.

  20. Quantitative Analysis and Modeling of 3-D TSV-Based Power Delivery Architectures

    NASA Astrophysics Data System (ADS)

    He, Huanyu

    As 3-D technology enters the commercial production stage, it is critical to understand different 3-D power delivery architectures on the stacked ICs and packages with through-silicon vias (TSVs). Appropriate design, modeling, analysis, and optimization approaches of the 3-D power delivery system are of foremost significance and great practical interest to the semiconductor industry in general. Based on fundamental physics of 3-D integration components, the objective of this thesis work is to quantitatively analyze the power delivery for 3D-IC systems, develop appropriate physics-based models and simulation approaches, understand the key issues, and provide potential solutions for design of 3D-IC power delivery architectures. In this work, a hybrid simulation approach is adopted as the major approach along with analytical method to examine 3-D power networks. Combining electromagnetic (EM) tools and circuit simulators, the hybrid approach is able to analyze and model micrometer-scale components as well as centimeter-scale power delivery system with high accuracy and efficiency. The parasitic elements of the components on the power delivery can be precisely modeled by full-wave EM solvers. Stack-up circuit models for the 3-D power delivery networks (PDNs) are constructed through a partition and assembly method. With the efficiency advantage of the SPICE circuit simulation, the overall 3-D system power performance can be analyzed and the 3-D power delivery architectures can be evaluated in a short computing time. The major power delivery issues are the voltage drop (IR drop) and voltage noise. With a baseline of 3-D power delivery architecture, the on-chip PDNs of TSV-based chip stacks are modeled and analyzed for the IR drop and AC noise. The basic design factors are evaluated using the hybrid approach, such as the number of stacked chips, the number of TSVs, and the TSV arrangement. Analytical formulas are also developed to evaluate the IR drop in 3-D chip stack in

  1. Sensitivity Analysis of the Scattering-Based SARBM3D Despeckling Algorithm.

    PubMed

    Di Simone, Alessio

    2016-01-01

    Synthetic Aperture Radar (SAR) imagery greatly suffers from multiplicative speckle noise, typical of coherent image acquisition sensors, such as SAR systems. Therefore, a proper and accurate despeckling preprocessing step is almost mandatory to aid the interpretation and processing of SAR data by human users and computer algorithms, respectively. Very recently, a scattering-oriented version of the popular SAR Block-Matching 3D (SARBM3D) despeckling filter, named Scattering-Based (SB)-SARBM3D, was proposed. The new filter is based on the a priori knowledge of the local topography of the scene. In this paper, an experimental sensitivity analysis of the above-mentioned despeckling algorithm is carried out, and the main results are shown and discussed. In particular, the role of both electromagnetic and geometrical parameters of the surface and the impact of its scattering behavior are investigated. Furthermore, a comprehensive sensitivity analysis of the SB-SARBM3D filter against the Digital Elevation Model (DEM) resolution and the SAR image-DEM coregistration step is also provided. The sensitivity analysis shows a significant robustness of the algorithm against most of the surface parameters, while the DEM resolution plays a key role in the despeckling process. Furthermore, the SB-SARBM3D algorithm outperforms the original SARBM3D in the presence of the most realistic scattering behaviors of the surface. An actual scenario is also presented to assess the DEM role in real-life conditions. PMID:27347971

  2. Sensitivity Analysis of the Scattering-Based SARBM3D Despeckling Algorithm

    PubMed Central

    Di Simone, Alessio

    2016-01-01

    Synthetic Aperture Radar (SAR) imagery greatly suffers from multiplicative speckle noise, typical of coherent image acquisition sensors, such as SAR systems. Therefore, a proper and accurate despeckling preprocessing step is almost mandatory to aid the interpretation and processing of SAR data by human users and computer algorithms, respectively. Very recently, a scattering-oriented version of the popular SAR Block-Matching 3D (SARBM3D) despeckling filter, named Scattering-Based (SB)-SARBM3D, was proposed. The new filter is based on the a priori knowledge of the local topography of the scene. In this paper, an experimental sensitivity analysis of the above-mentioned despeckling algorithm is carried out, and the main results are shown and discussed. In particular, the role of both electromagnetic and geometrical parameters of the surface and the impact of its scattering behavior are investigated. Furthermore, a comprehensive sensitivity analysis of the SB-SARBM3D filter against the Digital Elevation Model (DEM) resolution and the SAR image-DEM coregistration step is also provided. The sensitivity analysis shows a significant robustness of the algorithm against most of the surface parameters, while the DEM resolution plays a key role in the despeckling process. Furthermore, the SB-SARBM3D algorithm outperforms the original SARBM3D in the presence of the most realistic scattering behaviors of the surface. An actual scenario is also presented to assess the DEM role in real-life conditions. PMID:27347971

  3. Sensitivity Analysis of the Scattering-Based SARBM3D Despeckling Algorithm.

    PubMed

    Di Simone, Alessio

    2016-01-01

    Synthetic Aperture Radar (SAR) imagery greatly suffers from multiplicative speckle noise, typical of coherent image acquisition sensors, such as SAR systems. Therefore, a proper and accurate despeckling preprocessing step is almost mandatory to aid the interpretation and processing of SAR data by human users and computer algorithms, respectively. Very recently, a scattering-oriented version of the popular SAR Block-Matching 3D (SARBM3D) despeckling filter, named Scattering-Based (SB)-SARBM3D, was proposed. The new filter is based on the a priori knowledge of the local topography of the scene. In this paper, an experimental sensitivity analysis of the above-mentioned despeckling algorithm is carried out, and the main results are shown and discussed. In particular, the role of both electromagnetic and geometrical parameters of the surface and the impact of its scattering behavior are investigated. Furthermore, a comprehensive sensitivity analysis of the SB-SARBM3D filter against the Digital Elevation Model (DEM) resolution and the SAR image-DEM coregistration step is also provided. The sensitivity analysis shows a significant robustness of the algorithm against most of the surface parameters, while the DEM resolution plays a key role in the despeckling process. Furthermore, the SB-SARBM3D algorithm outperforms the original SARBM3D in the presence of the most realistic scattering behaviors of the surface. An actual scenario is also presented to assess the DEM role in real-life conditions.

  4. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    PubMed Central

    Morón, Carlos; Portilla, Marina P.; Somolinos, José A.; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  5. A fast and low-loss 3-D magnetotelluric inversion method with parallel structure

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Zhang, L.

    2013-12-01

    The 2D assumption is valid in some cases of interpretation, the approximation does not work in most cases, especially in areas with complex geo-electrical structure. A number of 3D magentotelluric inversion methods has been proposed, including RRI, CG, QA, NLCG. Each of those methods has its own advantages and disadvantages. However, as the 3D dataset and mesh grid require greater computer memory and calculation time than 2D methods, the efficiency of the inversion scheme become a key concern of 3D inversions. We chose NLCG as the optimization method for inversion. A parameter matrix related with the current resisitivity model and data error is proposed to approximate the Hessian matrix. So four forward calculation can be avoided each iteration. In addition, OPENMP parallel API is utilized to establish an effecient parallel inversion structure based on frequency to reduce computation time. And both synthetic and field data are used to test the efficiency of the inversion and the preconditioning method. The model consists of four square prisms residing in a halfspace. The total computation time of invertion is 706s (use one PC). Fiugre 1 shows the inversion result. The abnormal bodies can be distinguished clearly. Field data from the NIHE dataset in China is used to verify the reliability and efficiency of the 3D inversion method. The total computation time is about 25 minutes after 60 iterations on one PC. Totally, four electrical layers can be corresponded to the four stratum in 3D AMT inversion model, and the faults can be seen clearly. In addition, we can get more information about fault and alteration interface from constrained inversion result. Finally, the inversion method is very fast and low-loss, so it can be used in modern PC (need only one PC) with few hardware constraints. (a): initial model; (b): inversion depth slices (1-4km); (c): fitting error (a): AMT 3D slice; (b): CSAMT 2D model; (c): TEM 1D model; (d): SIP 2D model; (e) AMT 3D constrained

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

    NASA Astrophysics Data System (ADS)

    Dong, Jing; Bengtson, Kurt R.; Robinson, Barrett F.; Allebach, Jan P.

    2014-03-01

    Most of the 3D capture products currently in the market are high-end and pricey. They are not targeted for consumers, but rather for research, medical, or industrial usage. Very few aim to provide a solution for home and small business applications. Our goal is to fill in this gap by only using low-cost components to build a 3D capture system that can satisfy the needs of this market segment. In this paper, we present a low-cost 3D capture system based on the structured-light method. The system is built around the HP TopShot LaserJet Pro M275. For our capture device, we use the 8.0 Mpixel camera that is part of the M275. We augment this hardware with two 3M MPro 150 VGA (640 × 480) pocket projectors. We also describe an analytical approach to predicting the achievable resolution of the reconstructed 3D object based on differentials and small signal theory, and an experimental procedure for validating that the system under test meets the specifications for reconstructed object resolution that are predicted by our analytical model. By comparing our experimental measurements from the camera-projector system with the simulation results based on the model for this system, we conclude that our prototype system has been correctly configured and calibrated. We also conclude that with the analytical models, we have an effective means for specifying system parameters to achieve a given target resolution for the reconstructed object.

  7. Quantitative underwater 3D motion analysis using submerged video cameras: accuracy analysis and trajectory reconstruction.

    PubMed

    Silvatti, Amanda P; Cerveri, Pietro; Telles, Thiago; Dias, Fábio A S; Baroni, Guido; Barros, Ricardo M L

    2013-01-01

    In this study we aim at investigating the applicability of underwater 3D motion capture based on submerged video cameras in terms of 3D accuracy analysis and trajectory reconstruction. Static points with classical direct linear transform (DLT) solution, a moving wand with bundle adjustment and a moving 2D plate with Zhang's method were considered for camera calibration. As an example of the final application, we reconstructed the hand motion trajectories in different swimming styles and qualitatively compared this with Maglischo's model. Four highly trained male swimmers performed butterfly, breaststroke and freestyle tasks. The middle fingertip trajectories of both hands in the underwater phase were considered. The accuracy (mean absolute error) of the two calibration approaches (wand: 0.96 mm - 2D plate: 0.73 mm) was comparable to out of water results and highly superior to the classical DLT results (9.74 mm). Among all the swimmers, the hands' trajectories of the expert swimmer in the style were almost symmetric and in good agreement with Maglischo's model. The kinematic results highlight symmetry or asymmetry between the two hand sides, intra- and inter-subject variability in terms of the motion patterns and agreement or disagreement with the model. The two outcomes, calibration results and trajectory reconstruction, both move towards the quantitative 3D underwater motion analysis.

  8. Geometry of structures within crystalline bedrock constrained in