Science.gov

Sample records for 3d structural 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. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    PubMed Central

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

    2013-01-01

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

  3. 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.

  4. 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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Ge, Zhaoyang; Hu, Hong; Liu, Yanping

    2013-08-01

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

  7. 3D shape measurement of shoeprint impression with structured illumination and fringe pattern analysis

    NASA Astrophysics Data System (ADS)

    Su, Xianyu; Cao, Yiping; Xiang, Liqun; Chen, Wenjing

    2002-06-01

    The shoeprint impressions of suspect left at the crime scene can sometimes tell investigators what type of shoes to be looked for. These shoeprint impressions as one of the important evidence are useful in the detection of criminals. In this paper we propose a novel technique for identifying and analyzing the 3D characteristics of shoeprint impressions. We also design 3D shoeprint impression analysis system based on the combination the 3D shape measurement with structured illumination and fringe pattern analysis. We give a detail discussion on the principle and configuration of the system. Laboratory experiments show the technique is efficient in the detection of shoeprint and in the offering the reference for judicial evidence.

  8. A 3D moisture-stress FEM analysis for time dependent problems in timber structures

    NASA Astrophysics Data System (ADS)

    Fortino, Stefania; Mirianon, Florian; Toratti, Tomi

    2009-11-01

    This paper presents a 3D moisture-stress numerical analysis for timber structures under variable humidity and load conditions. An orthotropic viscoelastic-mechanosorptive material model is specialized on the basis of previous models. Both the constitutive model and the equations needed to describe the moisture flow across the structure are implemented into user subroutines of the Abaqus finite element code and a coupled moisture-stress analysis is performed for several types of mechanical loads and moisture changes. The presented computational approach is validated by analyzing some wood tests described in the literature and comparing the computational results with the reported experimental data.

  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. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    PubMed

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

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

    PubMed Central

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

    2009-01-01

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

  12. Structural description and combined 3D display for superior analysis of cerebral vascularity from MRA

    NASA Astrophysics Data System (ADS)

    Szekely, Gabor; Koller, Thomas; Kikinis, Ron; Gerig, Guido

    1994-09-01

    Medical image analysis has to support the clinicians ability to identify, manipulate and quantify anatomical structures. On scalar 2D image data, a human observer is often superior to computer assisted analysis, but the interpretation of vector- valued data or data combined from different modalities, especially in 3D, can benefit from computer assistance. The problem of how to convey the complex information to the clinician is often tackled by providing colored multimodality renderings. We propose to go a step beyond by supplying a suitable modelling of anatomical and functional structures encoding important shape features and physical properties. The multiple attributes regarding geometry, topology and function are carried by the symbolic description and can be interactively queried and edited. Integrated 3D rendering of object surfaces and symbolic representation acts as a visual interface to allow interactive communication between the observer and the complex data, providing new possibilities for quantification and therapy planning. The discussion is guided by the prototypical example of investigating the cerebral vasculature in MRA volume data. Geometric, topological and flow-related information can be assessed by interactive analysis on a computer workstation, providing otherwise hidden qualitative and quantitative information. Several case studies demonstrate the potential usage for structure identification, definition of landmarks, assessment of topology for catheterization, and local simulation of blood flow.

  13. Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast

    PubMed Central

    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. PMID:25799503

  14. 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.

  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. 3D-graphite structure

    SciTech Connect

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

    2011-01-15

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

  18. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  19. Analysis of the rupture process of the 1995 Kobe earthquake using a 3D velocity structure

    NASA Astrophysics Data System (ADS)

    Guo, Yujia; Koketsu, Kazuki; Ohno, Taichi

    2013-12-01

    A notable feature of the 1995 Kobe (Hyogo-ken Nanbu) earthquake is that violent ground motions occurred in a narrow zone. Previous studies have shown that the origin of such motions can be explained by the 3D velocity structure in this zone. This indicates not only that the 3D velocity structure significantly affects strong ground motions, but also that we should consider its effects in order to determine accurately the rupture process of the earthquake. Therefore, we have performed a joint source inversion of strong-motion, geodetic, and teleseismic data, where 3D Green's functions were calculated for strong-motion and geodetic data in the Osaka basin. Our source model estimates the total seismic moment to be about 2.1 × 1019 N m and the maximum slip reaches 2.9 m near the hypocenter. Although the locations of large slips are similar to those reported by Yoshida et al. (1996), there are quantitative differences between our results and their results due to the differences between the 3D and 1D Green's functions. We have also confirmed that our source model realized a better fit to the strong motion observations, and a similar fit as Yoshida et al. (1996) to the observed static displacements.

  20. Structural analysis of San Leo (RN, Italy) east and north cliffs using 3D point clouds

    NASA Astrophysics Data System (ADS)

    Spreafico, Margherita Cecilia; Bacenetti, Marco; Borgatti, Lisa; Cignetti, Martina; Giardino, Marco; Perotti, Luigi

    2013-04-01

    The town of San Leo, like many others in the historical region of Montefeltro (Northern Apennines, Italy), was built in medieval period on a calcarenite and sandstone slab, bordered by subvertical and overhanging cliffs up to 100 m high, for defense purposes. The slab and the underlying clayey substratum show widespread landslide phenomena: the first is tectonized and crossed by joints and faults, and it is affected by lateral spreading with associated rock falls, topples and tilting. Moreover, the underlying clayey substratum is involved in plastic movements, like earth flows and slides. The main cause of instability in the area, which brings about these movements, is the high deformability contrast between the plate and the underlying clays. The aim of our research is to set up a numerical model that can well describe the processes and take into account the different factors that influence the evolution of the movements. One of these factors is certainly the structural setting of the slab, characterized by several joints and faults; in order to better identify and detect the main joint sets affecting the study area a structural analysis was performed. Up to date, a series of scans of San Leo cliff taken in 2008 and 2011, with a Riegl Z420i were analyzed. Initially, we chose a test area, located in the east side of the cliff, in which analyses were performed using two different softwares: COLTOP 3D and Polyworks. We repeated the analysis using COLTOP for all the east wall and for a part of the north wall, including an area affected by a rock fall in 2006. In the test area we identified five sets with different dips and dip directions. The analysis of the east and north walls permitted to identify eight sets (seven plus the bedding) of discontinuities. We compared these results with previous ones from surveys taken by others authors in some areas and with some preliminary data from a traditional geological survey of the whole area. With traditional methods only a

  1. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    PubMed Central

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis.

    PubMed

    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 . PMID:25261217

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

    NASA Astrophysics Data System (ADS)

    Orduña, Agustin; Ayala, A. Gustavo

    2015-12-01

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

  10. 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)

  11. 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%.

  12. 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 .

  13. 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.

  14. 3D and Multispectral Imaging For Subcutaneous Structures Classification And Analysis

    SciTech Connect

    Paquit, Vincent C; Tobin Jr, Kenneth William; Price, Jeffery R; Meriaudeau, Fabrice

    2009-01-01

    A classification method to differentiate subcutaneous structures is presented. To obtain characteristic spectral signatures, we are investigating light propagation phenomena in biological tissues by combining visible to near-infrared multi-wavelength skin imaging and three dimensional topographic imaging of the skin surface.

  15. Automatic segmentation of solitary pulmonary nodules based on local intensity structure analysis and 3D neighborhood features in 3D chest CT images

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Kitasaka, Takayuki; Honma, Hirotoshi; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Mori, Kensaku

    2012-03-01

    This paper presents a solitary pulmonary nodule (SPN) segmentation method based on local intensity structure analysis and neighborhood feature analysis in chest CT images. Automated segmentation of SPNs is desirable for a chest computer-aided detection/diagnosis (CAS) system since a SPN may indicate early stage of lung cancer. Due to the similar intensities of SPNs and other chest structures such as blood vessels, many false positives (FPs) are generated by nodule detection methods. To reduce such FPs, we introduce two features that analyze the relation between each segmented nodule candidate and it neighborhood region. The proposed method utilizes a blob-like structure enhancement (BSE) filter based on Hessian analysis to augment the blob-like structures as initial nodule candidates. Then a fine segmentation is performed to segment much more accurate region of each nodule candidate. FP reduction is mainly addressed by investigating two neighborhood features based on volume ratio and eigenvector of Hessian that are calculates from the neighborhood region of each nodule candidate. We evaluated the proposed method by using 40 chest CT images, include 20 standard-dose CT images that we randomly chosen from a local database and 20 low-dose CT images that were randomly chosen from a public database: LIDC. The experimental results revealed that the average TP rate of proposed method was 93.6% with 12.3 FPs/case.

  16. 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.

  17. 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

  18. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

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

    2016-07-01

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

  19. 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.

  20. 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.

  1. Double Parton Scattering and 3D Proton Structure: A Light-Front Analysis

    NASA Astrophysics Data System (ADS)

    Rinaldi, Matteo; Scopetta, Sergio; Traini, Marco; Vento, Vicente

    2016-06-01

    Double parton scattering, occurring in high energy hadron-hadron collisions, e.g. at the LHC, is usually investigated through model dependent analyses of the so called effective cross section {σ_{eff}}. We present a dynamic approach to this fundamental quantity making use of a Light-Front model treatment. Within such a framework {σ_{eff}} is initially evaluated at low energy scale using the model and then, through QCD evolution, at high energy scale to reach the experimental conditions. Our numerical outcomes are consistent with the present experimental analyses of data in kinematical region we investigate. An important result of the present work is the {x_i} dependence of {σ_{eff}}, a feature directly connected to double parton correlations and which could unveil new information on the three dimensional structure of the proton.

  2. 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

  3. 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.

  4. Mesomechanical analysis of the ELASTO-PLASTIC behavior of a 3D composite-structure under tension

    NASA Astrophysics Data System (ADS)

    Romanova, V. A.; Soppa, E.; Schmauder, S.; Balokhonov, R. R.

    2005-11-01

    In this contribution, a mesomechanical approach to simulate the mechanical behavior with explicit consideration of the three-dimensional structure is applied to study the elasto-plastic response of a metal matrix composite material under tension. A procedure of a step-by-step packing (SSP) of a finite volume with structural elements has been used to design the composite structure consisting of an Al(6061)-matrix with Al2O3-inclusions. A three-dimensional mechanical problem of the structure behavior under tension has been solved numerically, using both an implicit finite-element method and an explicit finite-difference code. Special attention is given to the comparison of quasistatic and dynamic calculations. Evolution of plastic deformation in the matrix during tensile loading has been investigated. Qualitative and quantitative analysis of different components of stress and strain tensors is provided on the basis of mesomechanical concepts. Basing on the 3D-analysis, some conclusions regarding an applicability of a 2D approximation when considering deformation behavior on meso and macro scale levels have been done.

  5. In silico 3D structure analysis accelerates the solution of a real viral structure and antibodies docking mechanism

    PubMed Central

    Miki, Motohiro; Katayama, Kazuhiko

    2012-01-01

    Norwalk virus (NoV) is responsible for most outbreaks of non-bacterial gastroenteritis. NoV is genetically diverse and show antigenically variable. Recently, we produced a monoclonal antibody called 5B-18 that reacts broadly with NoV genogroup II (GII). We suspected the 5B-18 binds to a conformational epitope on 3D structure of virion. X-ray crystallography showed us that 5B-18 binds to NoV at the P domain, which protrudes from the capsid surface of the virion. However, there seems to be no space that would allow the IgG to approach the virion. To solve this problem, we used cryo-electron microscopy to examine NoV GII virus-like particles (VLPs). The P domain rises up higher in NoV GII than in NoV GI, and it seems to form an outer layer around the virion. Finally, using in silico modeling we found the 5B-18 Fab arms and NoV P region are quite flexible, so that 5B-18 can bind the NoV virion from bottom of P domain. This study demonstrates the shortcomings of studying biological phenomenon by only one technique. Each method has limitations. Multiple methods and modeling in silico are the keys to solving structural problems. PMID:23133439

  6. 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

  7. 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

  8. 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

  9. A new method for detecting colonic polyps based on local intensity structure analysis from 3D abdominal CT images

    NASA Astrophysics Data System (ADS)

    Oda, Masahiro; Nakada, Yuichi; Kitasaka, Takayuki; Mori, Kensaku; Suenaga, Yasuhito; Takayama, Tetsuji; Takabatake, Hirotsugu; Mori, Masaki; Natori, Hiroshi; Nawano, Shigeru

    2007-03-01

    This paper presents a new method for detecting colonic polyps from abdominal CT images based on Hessian matrix analysis. Recently, virtual colonoscopy (VC) has widely received attention as a new and less-invasive colon diagnostic method. A physician diagnoses the inside of the colon using a virtual colonoscopy system. However, since the colon has many haustra and its shape is long and convoluted, a physician has to change viewpoints and viewing directions of the virtual camera many times while diagnosing. Lesions behind haustra may be overlooked. Thus this paper proposes an automated colonic polyp detection method from 3D abdominal CT images. Colonic polyps are located on the colonic wall, and their CT values are higher than colonic lumen regions. In addition, CT values inside polyps tend to gradually increase from outward to inward (blob-like structure). We employ a blob structure enhancement filter based on the eigenvalues of a Hessian matrix to detect polyps with the above blob-shaped characteristics. For reducing FPs, we eliminate polyp candidate regions in which the maximum output value of the blob structure enhancement filter is smaller than given threshold values. Also small regions are removed from candidates. We applied the proposed method to 23 cases of abdominal CT images. Overall, 74.4% of the polyps were detected with 3.8 FPs per case.

  10. 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.

  11. 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

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

    PubMed

    Zhang, Yi; Huang, Haiyun; Dong, Xiaoqing; Fang, Yiliang; Wang, Kejing; Zhu, Lijuan; Wang, Ke; Huang, Tao; Yang, Jialiang

    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

  13. Accuracy in Quantitative 3D Image Analysis

    PubMed Central

    Bassel, George W.

    2015-01-01

    Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data. PMID:25804539

  14. 3D structure analysis of PAKs: A clue to the rational design for affinity reagents and blockers.

    PubMed

    Jha, Ramesh K; Strauss, Charlie E M

    2012-04-01

    The p21-activated kinase (PAK) family plays a versatile role in cell signaling by forming a hub of interactions. PAKs bind the GTPases like RAC and CDC42. Their proline-rich motifs bind SH3 adaptor proteins such as PIX and NCK. PAKs display nuclear localization signal sites and a potential Integrin binding site. No fully complete structure of the PAKs has been published; partial 3D structures of the PAK family kinases include portions of the auto-inhibited PAK1, GTPase bound to small peptides from PAKs, and the kinase domains from PAK1 and PAK4-6 (with small ligands in a few cases). This review focuses on exploring the intermolecular interaction regions in these 3D structures and we offer insights on the missing regions in crystal structure of the auto-inhibited PAK1. Understanding and modulation of PAK intermolecular interactions can pave the way for PAK blockers and biosensors. PMID:23162739

  15. 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

  16. Inferential modeling of 3D chromatin structure

    PubMed Central

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-01-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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…

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

    PubMed

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

    2008-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  5. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

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

  6. 3D surface defect analysis and evaluation

    NASA Astrophysics Data System (ADS)

    Yang, B.; Jia, M.; Song, G. J.; Tao, L.; Harding, K. G.

    2008-08-01

    A method is proposed for surface defect analysis and evaluation. Good 3D point clouds can now be obtained through a variety of surface profiling methods such as stylus tracers, structured light, or interferometry. In order to inspect a surface for defects, first a reference surface that represents the surface without any defects needs to be identified. This reference surface can then be fit to the point cloud. The algorithm we present finds the least square solution for the overdetermined equation set to obtain the parameters of the reference surface mathematical description. The distance between each point within the point cloud and the reference surface is then calculated using to the derived reference surface equation. For analysis of the data, the user can preset a threshold distance value. If the calculated distance is bigger than the threshold value, the corresponding point is marked as a defect point. The software then generates a color-coded map of the measured surface. Defect points that are connected together are formed into a defect-clustering domain. Each defect-clustering domain is treated as one defect area. We then use a clustering domain searching algorithm to auto-search all the defect areas in the point cloud. The different critical parameters used for evaluating the defect status of a point cloud that can be calculated are described as: P-Depth,a peak depth of all defects; Defect Number, the number of surface defects; Defects/Area, the defect number in unit area; and Defect Coverage Ratio which is a ratio of the defect area to the region of interest.

  7. 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

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

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

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

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

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-11-16

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

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

    PubMed

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

    2015-07-01

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

  11. 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

  12. 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

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

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  15. 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

  16. 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

  17. USJ metrology: from 0D to 3D analysis

    SciTech Connect

    Vandervorst, Wilfried

    2007-09-26

    The analysis of ultra shallow junctions is becoming a challenging task for which numerous tools and concepts are available. The requirements range from a simple 0D-analysis such as the integral dose or the sheet resistance over a simple 1D-profile (as obtained on blanket films) towards the 2D-dopant profile within a transistor. The ultimate complexity will be the analysis of a complete 3D-structure such as a FINFET, requiring a metrology tool with 3D-resolution. In each of these areas significant progress has been made in recent years and new concepts are emerging which will be discussed in this review.

  18. 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.

  19. 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

  20. Automatic abdominal lymph node detection method based on local intensity structure analysis from 3D x-ray CT images

    NASA Astrophysics Data System (ADS)

    Nakamura, Yoshihiko; Nimura, Yukitaka; Kitasaka, Takayuki; Mizuno, Shinji; Furukawa, Kazuhiro; Goto, Hidemi; Fujiwara, Michitaka; Misawa, Kazunari; Ito, Masaaki; Nawano, Shigeru; Mori, Kensaku

    2013-03-01

    This paper presents an automated method of abdominal lymph node detection to aid the preoperative diagnosis of abdominal cancer surgery. In abdominal cancer surgery, surgeons must resect not only tumors and metastases but also lymph nodes that might have a metastasis. This procedure is called lymphadenectomy or lymph node dissection. Insufficient lymphadenectomy carries a high risk for relapse. However, excessive resection decreases a patient's quality of life. Therefore, it is important to identify the location and the structure of lymph nodes to make a suitable surgical plan. The proposed method consists of candidate lymph node detection and false positive reduction. Candidate lymph nodes are detected using a multi-scale blob-like enhancement filter based on local intensity structure analysis. To reduce false positives, the proposed method uses a classifier based on support vector machine with the texture and shape information. The experimental results reveal that it detects 70.5% of the lymph nodes with 13.0 false positives per case.

  1. 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.

  2. 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

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

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

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

  4. 3-D object-oriented image analysis of geophysical data

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    Geophysical data are the main source of information about the subsurface. Geophysical techniques are, however, highly non-unique in determining specific physical parameters and boundaries of subsurface objects. To obtain actual physical information, an inversion process is often applied, in which measurements at or above the Earth surface are inverted into a 2- or 3-D subsurface spatial distribution of the physical property. Interpreting these models into structural objects, related to physical processes, requires a priori knowledge and expert analysis which is susceptible to subjective choices and is therefore often non-repeatable. In this research, we implemented a recently introduced object-based approach to interpret the 3-D inversion results of a single geophysical technique using the available a priori information and the physical and geometrical characteristics of the interpreted objects. The introduced methodology is semi-automatic and repeatable, and allows the extraction of subsurface structures using 3-D object-oriented image analysis (3-D OOA) in an objective knowledge-based classification scheme. The approach allows for a semi-objective setting of thresholds that can be tested and, if necessary, changed in a very fast and efficient way. These changes require only changing the thresholds used in a so-called ruleset, which is composed of algorithms that extract objects from a 3-D data cube. The approach is tested on a synthetic model, which is based on a priori knowledge on objects present in the study area (Tanzania). Object characteristics and thresholds were well defined in a 3-D histogram of velocity versus depth, and objects were fully retrieved. The real model results showed how 3-D OOA can deal with realistic 3-D subsurface conditions in which the boundaries become fuzzy, the object extensions become unclear and the model characteristics vary with depth due to the different physical conditions. As expected, the 3-D histogram of the real data was

  5. 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.

  6. 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.

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

    PubMed

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

    2014-09-23

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

  8. 3D precision surface measurement by dynamic structured light

    NASA Astrophysics Data System (ADS)

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

    2004-02-01

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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Acetylcholinesterase: From 3D Structure to Function

    PubMed Central

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

    2010-01-01

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

  14. 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.

  15. 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.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25159614

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

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

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

  18. Capacitance extraction from complex 3D interconnect structures

    SciTech Connect

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

    1999-06-01

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

  19. 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.

  20. 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.

  1. 3D Landslides Susceptibility Analysis in Romanian Subcarpathians

    NASA Astrophysics Data System (ADS)

    Sandric, Ionuc; Ilinca, Viorel; Chitu, Zenaida; Jurchescu, Marta

    2015-04-01

    Most of the present day studies make use the 2.5D raster data formats for the landslide susceptibility analysis at regional scales. This data format has some disadvantages when geological and lithological settings are spatial discretized, hence these disadvantages propagate in the landslides susceptibility analysis and especially where only surface lithology is used. The main disadvantage when using 3D data models for the assessment of landslide susceptibility at regional scales is represented by the quality of the geological and lithological information that is available for a depth of no more than 100m. In order to mitigate this, a sufficient number of boreholes is required and sometimes is not available. In order to overcome the lack of borehole data, our approach was to make use of the present-day geological maps at scales ranging from 1:25,000 to 1:50,000 and to generate a geological 3D model up to a depth of 100m. The geological model was generated based on expert knowledge interpretations and geological cross sections provided on these geological maps. Using the 3D geological model a more complex 3D model was generated for the landslide susceptibility analysis that also contains information from other predictor factors like slope gradient, land-cover and land-use. For the landslide susceptibility analysis instead of using map algebra equations on classic pixel based data sets, the equations were adapted for 3D data models and map algebra equations on voxels. The test sites are located in the areas of Romanian Subcarpathians. The Romanian Subcarpathians are located to the exterior of the Carpathians. They consist of a large variety of rocks, flysch-type deposits in the inner part and molasse deposits in the outer part, ranging from a Cretacic-Paleogene to a Quaternary age. While some parts of the Subcarpathians have a basic geology, with a monoclinal geological structure, other parts like the Curvature Subcarpathians, present acomplex folded and faulted

  2. 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.

  3. The 3D Radiation Dose Analysis For Satellite

    NASA Astrophysics Data System (ADS)

    Cai, Zhenbo; Lin, Guocheng; Chen, Guozhen; Liu, Xia

    2002-01-01

    hence, it is too simple to guide satellite radiation protection and ground experiments only based on the 1D radiation analysis results. To comprehend the radiation dose status of satellite adequately, it's essential to perform 3D radiation analysis for satellites. using computer software. From this 3D layout, the satellite model can be simplified appropriately. First select the point to be analyzed in the simplified satellite model, and extend many lines to the outside space, which divides the 4 space into many corresponding small areas with a certain solid angle. Then the shielding masses through the satellite equipment and structures along each direction are calculated, resulting in the shielding mass distribution in all space directions based on the satellite layout. Finally, using the relationship between radiation dose and shielding thickness from the 1D analysis, calculate the radiation dose in each area represented by each line. After we obtain the radiation dose and its space distribution for the point of interest, the 3D satellite radiation analysis is completed. radiation analysis based on satellite 3D CAD layout has larger benefit for engineering applications than the 1D analysis based on the solid sphere shielding model. With the 3D model, the analysis of space environment and its effect is combined closely with actual satellite engineering. The 3D radiation analysis not only provides valuable engineering data for satellite radiation design and protection, but also provides possibility to apply new radiation protection approaches, which expands technology horizon and broadens ways for technology development.

  4. 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.

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

    PubMed

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

    2016-07-01

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

  6. The 3D-based scaling index algorithm to optimize structure analysis of trabecular bone in postmenopausal women with and without osteoporotic spine fractures

    NASA Astrophysics Data System (ADS)

    Muller, Dirk; Monetti, Roberto A.; Bohm, Holger F.; Bauer, Jan; Rummeny, Ernst J.; Link, Thomas M.; Rath, Christoph W.

    2004-05-01

    The scaling index method (SIM) is a recently proposed non-linear technique to extract texture measures for the quantitative characterisation of the trabecular bone structure in high resolution magnetic resonance imaging (HR-MRI). The three-dimensional tomographic images are interpreted as a point distribution in a state space where each point (voxel) is defined by its x, y, z coordinates and the grey value. The SIM estimates local scaling properties to describe the nonlinear morphological features in this four-dimensional point distribution. Thus, it can be used for differentiating between cluster-, rod-, sheet-like and unstructured (background) image components, which makes it suitable for quantifying the microstructure of human cancellous bone. The SIM was applied to high resolution magnetic resonance images of the distal radius in patients with and without osteoporotic spine fractures in order to quantify the deterioration of bone structure. Using the receiver operator characteristic (ROC) analysis the diagnostic performance of this texture measure in differentiating patients with and without fractures was compared with bone mineral density (BMD). The SIM demonstrated the best area under the curve (AUC) value for discriminating the two groups. The reliability of our new texture measure and the validity of our results were assessed by applying bootstrapping resampling methods. The results of this study show that trabecular structure measures derived from HR-MRI of the radius in a clinical setting using a recently proposed algorithm based on a local 3D scaling index method can significantly improve the diagnostic performance in differentiating postmenopausal women with and without osteoporotic spine fractures.

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

    PubMed

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

    2012-01-21

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

  8. Designing 3D Structure by 5-7 Kirigami

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    PubMed

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

    2013-07-01

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

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Danis, Cara

    2012-01-01

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

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

    PubMed

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

    2016-07-01

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

  13. 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).

  14. 3D Seismic Imaging over a Potential Collapse Structure

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  15. 3D object-oriented image analysis in 3D geophysical modelling: Analysing the central part of the East African Rift System

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Non-uniqueness of satellite gravity interpretation has traditionally been reduced by using a priori information from seismic tomography models. This reduction in the non-uniqueness has been based on velocity-density conversion formulas or user interpretation of the 3D subsurface structures (objects) based on the seismic tomography models and then forward modelling these objects. However, this form of object-based approach has been done without a standardized methodology on how to extract the subsurface structures from the 3D models. In this research, a 3D object-oriented image analysis (3D OOA) approach was implemented to extract the 3D subsurface structures from geophysical data. The approach was applied on a 3D shear wave seismic tomography model of the central part of the East African Rift System. Subsequently, the extracted 3D objects from the tomography model were reconstructed in the 3D interactive modelling environment IGMAS+, and their density contrast values were calculated using an object-based inversion technique to calculate the forward signal of the objects and compare it with the measured satellite gravity. Thus, a new object-based approach was implemented to interpret and extract the 3D subsurface objects from 3D geophysical data. We also introduce a new approach to constrain the interpretation of the satellite gravity measurements that can be applied using any 3D geophysical model.

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

    PubMed

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

    2014-01-01

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

  17. 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.

  18. Instability and Wave Propagation in Structured 3D Composites

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  19. 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.

  20. 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

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

    PubMed

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

    2015-01-01

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

  2. 3D surface analysis and classification in neuroimaging segmentation.

    PubMed

    Zagar, Martin; Mlinarić, Hrvoje; Knezović, Josip

    2011-06-01

    This work emphasizes new algorithms for 3D edge and corner detection used in surface extraction and new concept of image segmentation in neuroimaging based on multidimensional shape analysis and classification. We propose using of NifTI standard for describing input data which enables interoperability and enhancement of existing computing tools used widely in neuroimaging research. In methods section we present our newly developed algorithm for 3D edge and corner detection, together with the algorithm for estimating local 3D shape. Surface of estimated shape is analyzed and segmented according to kernel shapes. PMID:21755723

  3. 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.

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

    PubMed Central

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

    2014-01-01

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

  5. 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.

  6. 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.

  7. Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-2-d1 and -3-d1

    SciTech Connect

    Craig, Norman C.; Chen, Yihui; van Besien, Herman; Blake, Thomas A.

    2014-09-01

    The 2-d1 and 3-d1 isotopologues of trans-hexatriene have been synthesized, and their high-resolution (0.0015 cm-1) IR spectra have been recorded. For each of the isotopologues the rotational structure in four C-type bands for out-of-plane vibrational modes has been analyzed, and the ground state combination differences (GSCDs) have been pooled. Ground state rotational constants have been fitted to the GSCDs. For the 2-d species, A0, B0, and C0 values of 0.7837254(5), 0.0442806(3), and 0.0419299(2) cm-1 were fitted to 2450 GSCDs. For the 3-d species, A0, B0, and C0 values of 0.7952226(8), 0.0446149(7), and 0.0422661(4) cm-1 were fitted to 2234 GSCDs. For the eleven out-of-plane modes of the two isotopologues, predictions of anharmonic wavenumbers and harmonic intensities have been computed and compared with experiment where possible.

  8. Accuracy of 3D scanners in tooth mark analysis.

    PubMed

    Molina, Ana; Martin-de-las-Heras, Stella

    2015-01-01

    The objective of this study was to compare the accuracy of contact and laser 3D scanners in tooth mark analysis. Ten dental casts were scanned with both 3D scanners. Seven linear measurements were made from the 3D images of dental casts and biting edges generated with DentalPrint© software (University of Granada, Granada, Spain). The uncertainty value for contact 3D scanning was 0.833 for the upper dental cast and 0.660 mm for the lower cast; similar uncertainty values were found for 3D-laser scanning. Slightly higher uncertainty values were obtained for the 3D biting edges generated. The uncertainty values for single measurements ranged from 0.1 to 0.3 mm with the exception of the intercanine distance, in which higher values were obtained. Knowledge of the error rate in the 3D scanning of dental casts and biting edges is especially relevant to be applied in practical forensic cases. PMID:25388960

  9. 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.

  10. 3D reconstruction methods of coronal structures by radio observations

    NASA Astrophysics Data System (ADS)

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

    1992-11-01

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

  11. 3D reconstruction methods of coronal structures by radio observations

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  12. 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.

  13. 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.

  14. 3-D simulation of nanopore structure for DNA sequencing.

    PubMed

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

    2012-07-01

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

  15. 3-D lookup: Fast protein structure database searches

    SciTech Connect

    Holm. L.; Sander, C.

    1995-12-31

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

  16. 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.

  17. 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.

  18. 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.

  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. 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)

  1. 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. PMID:26700045

  2. 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.

  3. Engineering extracellular matrix structure in 3D multiphase tissues

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2016-05-01

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

  5. Time Series Analysis of 3D Coordinates Using Nonstochastic Observations

    NASA Astrophysics Data System (ADS)

    Velsink, Hiddo

    2016-03-01

    Adjustment and testing of a combination of stochastic and nonstochastic observations is applied to the deformation analysis of a time series of 3D coordinates. Nonstochastic observations are constant values that are treated as if they were observations. They are used to formulate constraints on the unknown parameters of the adjustment problem. Thus they describe deformation patterns. If deformation is absent, the epochs of the time series are supposed to be related via affine, similarity or congruence transformations. S-basis invariant testing of deformation patterns is treated. The model is experimentally validated by showing the procedure for a point set of 3D coordinates, determined from total station measurements during five epochs. The modelling of two patterns, the movement of just one point in several epochs, and of several points, is shown. Full, rank deficient covariance matrices of the 3D coordinates, resulting from free network adjustments of the total station measurements of each epoch, are used in the analysis.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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. PMID:27037463

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

    NASA Astrophysics Data System (ADS)

    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.

  12. 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

  13. 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.

  14. 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

  15. Numerical analysis of 3-D potential flow in centrifugal turbomachines

    NASA Astrophysics Data System (ADS)

    Daiguji, H.

    1983-09-01

    A numerical method is developed for analysing a three-dimensional steady incompressible potential flow through an impeller in centrifugal turbomachines. The method is the same as the previous method which was developed for the axial flow turbomachines, except for some treatments in the downstream region. In order to clarify the validity and limitation of the method, a comparison with the existing experimental data and numerical results is made for radial flow compressor impellers. The calculated blade surface pressure distributions almost coincide with the quasi-3-D calculation by Krimerman and Adler (1978), but are different partly from the quasi-3-D calculation using one meridional flow analysis. It is suggested from this comparison that the flow through an impeller with high efficiency near the design point can be predicted by this fully 3-D numerical method.

  16. Protein 3D Structure Computed from Evolutionary Sequence Variation

    PubMed Central

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

    2011-01-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. SNR analysis of 3D magnetic resonance tomosynthesis (MRT) imaging

    NASA Astrophysics Data System (ADS)

    Kim, Min-Oh; Kim, Dong-Hyun

    2012-03-01

    In conventional 3D Fourier transform (3DFT) MR imaging, signal-to-noise ratio (SNR) is governed by the well-known relationship of being proportional to the voxel size and square root of the imaging time. Here, we introduce an alternative 3D imaging approach, termed MRT (Magnetic Resonance Tomosynthesis), which can generate a set of tomographic MR images similar to multiple 2D projection images in x-ray. A multiple-oblique-view (MOV) pulse sequence is designed to acquire the tomography-like images used in tomosynthesis process and an iterative back-projection (IBP) reconstruction method is used to reconstruct 3D images. SNR analysis is performed and shows that resolution and SNR tradeoff is not governed as with typical 3DFT MR imaging case. The proposed method provides a higher SNR than the conventional 3D imaging method with a partial loss of slice-direction resolution. It is expected that this method can be useful for extremely low SNR cases.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

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

  7. Triangular framework mesh generation of 3D geological structure

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  8. 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

  9. 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

  10. 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

  11. A Framework for 3D Vessel Analysis using Whole Slide Images of Liver Tissue Sections

    PubMed Central

    Liang, Yanhui; Wang, Fusheng; Treanor, Darren; Magee, Derek; Roberts, Nick; Teodoro, George; Zhu, Yangyang; Kong, Jun

    2015-01-01

    Three-dimensional (3D) high resolution microscopic images have high potential for improving the understanding of both normal and disease processes where structural changes or spatial relationship of disease features are significant. In this paper, we develop a complete framework applicable to 3D pathology analytical imaging, with an application to whole slide images of sequential liver slices for 3D vessel structure analysis. The analysis workflow consists of image registration, segmentation, vessel cross-section association, interpolation, and volumetric rendering. To identify biologically-meaningful correspondence across adjacent slides, we formulate a similarity function for four association cases. The optimal solution is then obtained by constrained Integer Programming. We quantitatively and qualitatively compare our vessel reconstruction results with human annotations. Validation results indicate a satisfactory concordance as measured both by region-based and distance-based metrics. These results demonstrate a promising 3D vessel analysis framework for whole slide images of liver tissue sections. PMID:27034719

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

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

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

  13. 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.

  14. 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

  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. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 3D structures of membrane proteins from genomic sequencing

    PubMed Central

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

    2012-01-01

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

  3. 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.

  4. 3D structure/function analysis of PilX reveals how minor pilins can modulate the virulence properties of type IV pili

    PubMed Central

    Helaine, Sophie; Dyer, David H.; Nassif, Xavier; Pelicic, Vladimir; Forest, Katrina T.

    2007-01-01

    Type IV pili (Tfp) are widespread filamentous bacterial organelles that mediate multiple virulence-related phenotypes. They are composed mainly of pilin subunits, which are processed before filament assembly by dedicated prepilin peptidases. Other proteins processed by these peptidases, whose molecular nature and mode of action remain enigmatic, play critical roles in Tfp biology. We have performed a detailed structure/function analysis of one such protein, PilX from Neisseria meningitidis, which is crucial for formation of bacterial aggregates and adhesion to human cells. The x-ray crystal structure of PilX reveals the α/β roll fold shared by all pilins, and we show that this protein colocalizes with Tfp. These observations suggest that PilX is a minor, or low abundance, pilin that assembles within the filaments in a similar way to pilin. Deletion of a PilX distinctive structural element, which is predicted to be exposed on the filament surface, abolishes aggregation and adhesion. Our results support a model in which surface-exposed motifs in PilX subunits stabilize bacterial aggregates against the disruptive force of pilus retraction and illustrate how a minor pilus component can enhance the functional properties of pili of rather simple composition and structure. PMID:17893339

  5. Advanced Visualization and Analysis of Climate Data using DV3D and UV-CDAT

    NASA Astrophysics Data System (ADS)

    Maxwell, T. P.

    2012-12-01

    This paper describes DV3D, a Vistrails package of high-level modules for the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) interactive visual exploration system that enables exploratory analysis of diverse and rich data sets stored in the Earth System Grid Federation (ESGF). DV3D provides user-friendly workflow interfaces for advanced visualization and analysis of climate data at a level appropriate for scientists. The application builds on VTK, an open-source, object-oriented library, for visualization and analysis. DV3D provides the high-level interfaces, tools, and application integrations required to make the analysis and visualization power of VTK readily accessible to users without exposing burdensome details such as actors, cameras, renderers, and transfer functions. It can run as a desktop application or distributed over a set of nodes for hyperwall or distributed visualization applications. DV3D is structured as a set of modules which can be linked to create workflows in Vistrails. Figure 1 displays a typical DV3D workflow as it would appear in the Vistrails workflow builder interface of UV-CDAT and, on the right, the visualization spreadsheet output of the workflow. Each DV3D module encapsulates a complex VTK pipeline with numerous supporting objects. Each visualization module implements a unique interactive 3D display. The integrated Vistrails visualization spreadsheet offers multiple synchronized visualization displays for desktop or hyperwall. The currently available displays include volume renderers, volume slicers, 3D isosurfaces, 3D hovmoller, and various vector plots. The DV3D GUI offers a rich selection of interactive query, browse, navigate, and configure options for all displays. All configuration operations are saved as Vistrails provenance. DV3D's seamless integration with UV-CDAT's climate data management system (CDMS) and other climate data analysis tools provides a wide range of climate data analysis operations, e

  6. Computerized 3D morphological analysis of glenoid orientation.

    PubMed

    Ghafurian, Soheil; Galdi, Balazs; Bastian, Sevag; Tan, Virak; Li, Kang

    2016-04-01

    An accurate preoperative measurement of glenoid orientation is crucial for evaluating pathologies and successful total shoulder arthroplasty. Existing methods may be labor-intensive, observer-dependent, and sensitive to the misalignment between the scapula plane and CT scanning direction. In this study, we proposed a computation framework and performed an automated analysis of the glenoid orientation based on 3D surface data. Three-dimensional models of 12 scapulae were analyzed. The glenoid cavity and external anatomical features were automatically extracted from these 3D models. Glenoid version was calculated using the scapula plane and the fulcrum axis alternatively. Glenoid inclination was measured both relative to transverse axis of the scapula and the medial pole-inferior tip axis. The mean (±SD) of the fulcrum-based glenoid version was -0.55° (±4.17°), while the scapular-plane-based glenoid version was -5.05° (±3.50°). The mean (±SD) of glenoid inclinations based on the medial pole and inferior tip was 12.75° (±5.03°) while the mean (±SD) of the glenoid inclination based on the medial pole and glenoid center was 4.63° (±4.86°). Our computational framework was able to extract the reproducible morphological measures free of inter- and intra- observer variability. For the first time in 3D, we showed that the fulcrum axis was practically perpendicular to the glenoid plane normal (radial line), and thus extended the fulcrum-based glenoid version for quantifying 3D glenoid orientation. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:692-698, 2016. PMID:26400654

  7. 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

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

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

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

  14. 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

  15. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

    PubMed Central

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

    2015-01-01

    Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions. PMID:25940394

  16. 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.

  17. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

    DOE PAGESBeta

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

    2015-05-05

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

  18. Triangulation Based 3D Laser Imaging for Fracture Orientation Analysis

    NASA Astrophysics Data System (ADS)

    Mah, J.; Claire, S.; Steve, M.

    2009-05-01

    sets (strike/dip: 060/00, 114/86) were identified from 49 manual inclinometer measurements A stereonet of joint poles from the 3D laser data was generated using the commercial software Split-FX. Joint sets were identified successfully and their orientations correlated well with the hand measurements. However, Split-Fx overlays a simply 2D grid of equal-sized triangles onto the 3D surface and requires significant user input. In a more automated approach, we have developed a MATLAB script which directly imports the Polyworks 3D triangular mesh. A typical mesh is composed of over 1 million triangles of variable sizes: smooth regions are represented by large triangles, whereas rough surfaces are captured by several smaller triangles. Using the triangle vertices, the script computes the strike and dip of each triangle. This approach opens possibilities for statistical analysis of a large population of fracture orientation estimates, including surface texture. The methodology will be used to evaluate both synthetic and field data.

  19. 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.

  20. 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

  1. 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.

  2. 3D geometric analysis of the aorta in 3D MRA follow-up pediatric image data

    NASA Astrophysics Data System (ADS)

    Wörz, Stefan; Alrajab, Abdulsattar; Arnold, Raoul; Eichhorn, Joachim; von Tengg-Kobligk, Hendrik; Schenk, Jens-Peter; Rohr, Karl

    2014-03-01

    We introduce a new model-based approach for the segmentation of the thoracic aorta and its main branches from follow-up pediatric 3D MRA image data. For robust segmentation of vessels even in difficult cases (e.g., neighboring structures), we propose a new extended parametric cylinder model which requires only relatively few model parameters. The new model is used in conjunction with a two-step fitting scheme for refining the segmentation result yielding an accurate segmentation of the vascular shape. Moreover, we include a novel adaptive background masking scheme and we describe a spatial normalization scheme to align the segmentation results from follow-up examinations. We have evaluated our proposed approach using different 3D synthetic images and we have successfully applied the approach to follow-up pediatric 3D MRA image data.

  3. 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.

  4. 3D ESPI and 3D shearography measurements applied to NDT and FEM analysis validation for industrial quality control

    NASA Astrophysics Data System (ADS)

    Hack, Erwin K.; Riner, Marc

    2001-10-01

    Laser interferometric methods opened the way to measure displacements and deformations of an object in a while- field, non-contact and 3D manner. Therefore, they are used in non-destructive testing and validation of 3D finite element (FE) simulation results. This paper emphasizes the fact that the process of validating an FE result comprises in turn the validation and assessment of the optical measurement method and the experimental bou8ndary condition. Application examples for FE analysis validation and NDT from machine engineering, space technology, and biomedical engineering are presented.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2015-12-01

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

  7. 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

  8. 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.

  9. 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. PMID:27015664

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  12. Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP.

    PubMed

    Müller, Martina; Deimling, Tobias; Hopfner, Karl-Peter; Witte, Gregor

    2015-08-01

    The identification of the essential bacterial second messenger cyclic-di-AMP (c-di-AMP) synthesized by the DNA-integrity scanning protein A (DisA) has opened up a new and emerging field in bacterial signalling. To further analyse the diadenylate cyclase (DAC) reaction catalysed by the DAC domains of DisA, we crystallized Thermotoga maritima DisA in the presence of different ATP analogues and metal ions to identify the metal-binding site and trap the enzyme in pre- and post-reaction states. Through structural and biochemical assays we identified important residues essential for the reaction in the active site of the DAC domains. Our structures resolve the metal-binding site and thus explain the activation of ATP for the DAC reaction. Moreover, we were able to identify a potent inhibitor of the DAC domain. Based on the available structures and homology to annotated DAC domains we propose a common mechanism for c-di-AMP synthesis by DAC domains in c-di-AMP-producing species and a possible approach for its effective inhibition. PMID:26014055

  13. Analysis of 3d complex structure and heterogeneity effects on formation and propagation of regional phases in Eurasia. Final report, 15 August 1992-30 September 1994

    SciTech Connect

    Lay, T.; Wu, R.S.

    1994-12-13

    This document is the final report for this grant to develop new three-dimensional wave propagation techniques for high frequency waves in heterogeneous media. The report is divided into four sections, each being a published paper sponsored by this grant. In the first section we formulate a one-way wide-angle elastic wave propagation method for arbitrarily heterogeneous media in both the space and wavenumber domains using elastic Rayleigh integrals and local elastic Born scattering theory. In the second section this complex phase screen method is compared with fourth-order finite differences and exact eigenfunction expansion calculations for two-dimensional inhomogeneous media to assess the accuracy of the one-way propagation algorithm. In the third section, an observational study of continental margin structure influence on Lg propagation is presented, using data from the former Soviet stations for nuclear explosions at Novaya Zemlya. We find that bathymetric features can be correlated with energy levels of Lg, suggesting that waveguide structure influences regional phase energy partitioning. This idea is pursued in the fourth section, using Eurasian earthquake and nuclear explosion data along with information about the crustal structure in Eurasia. We develop empirical relations that reduce the scatter in the P/Lg discriminant at low frequency.

  14. 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

  15. 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

  16. 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.

  17. 3D scanning of internal structure in gel engineering materials with visual scanning microscopic light scattering

    NASA Astrophysics Data System (ADS)

    Watanabe, Yosuke; Gong, Jing; Masato, Makino; Kabir, M. Hasnat; Furukawa, Hidemitsu

    2014-04-01

    The 3D printing technology, causing much attention from the beginning of 2013, will be possibly an alternative method to fabricate the biological soft tissues. Recently our group of Yamagata University has developed the world-first 3D Gel Printer to fabricate the complicated gel-materials with high-strength and biocompatibility. However, there are no 3D scanners that collect the data from the internal structure of complicated gel objects such as eye lens. It means that a new system for scanning the internal structure is needed now. In this study, firstly, we have tried to investigate the gel network of synthetic and biological gel with scanning microscopic light scattering (SMILS). We calculated the Young's modulus of synthetic gels with the SMILS and with the tensile test, and precisely compared the results between them. The temperature dependences of the inside structure and the transparency are observed in the pig crystalline lens. The quantitative analysis indicates the importance of the internal structure of real object. Secondary, we show the new system named Gel-scanner that can provide the 2-dimentional data of the internal structure. From examining our findings, the scanning of internal structure will enable us to expect physical properties of the real object. We convince that the gelscanner will play major role in the various fields.

  18. Structure and Metabolic-Flow Analysis of Molecular Complexity in a (13) C-Labeled Tree by 2D and 3D NMR.

    PubMed

    Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant. PMID:27060701

  19. 3D morphology of the human hepatic ferritin mineral core: New evidence for a subunit structure revealed by single particle analysis of HAADF-STEM images

    PubMed Central

    Pan, Ying-Hsi; Sader, Kasim; Powell, Jonathan J.; Bleloch, Andrew; Gass, Mhairi; Trinick, John; Warley, Alice; Li, Andy; Brydson, Rik; Brown, Andy

    2009-01-01

    Ferritin, the major iron storage protein, has dual functions; it sequesters redox activity of intracellular iron and facilitates iron turn-over. Here we present high angle annular dark field (HAADF) images from individual hepatic ferritin cores within tissue sections, these images were obtained using spherical aberration corrected scanning transmission electron microscopy (STEM) under controlled electron fluence. HAADF images of the cores suggest a cubic morphology and a polycrystalline (ferrihydrite) subunit structure that is not evident in equivalent bright field images. By calibrating contrast levels in the HAADF images using quantitative electron energy loss spectroscopy, we have estimated the absolute iron content in any one core, and produced a three dimensional reconstruction of the average core morphology. The core is composed of up to eight subunits, consistent with the eight channels in the protein shell that deliver iron to the central cavity. We find no evidence of a crystallographic orientation relationship between core subunits. Our results confirm that the ferritin protein shell acts as a template for core morphology and within the core, small (∼2 nm), surface-disordered ferrihydrite subunits connect to leave a low density centre and a high surface area that would allow rapid turn-over of iron in biological systems. PMID:19116170

  20. A Numerical Analysis of 3D EM Imaging from a Single Borehole

    SciTech Connect

    Alumbaugh, David L.; Wilt, Michael J.

    1999-07-27

    In this study we analyze the feasibility of three dimensional (3D) electromagnetic (EM) imaging from a single borehole. The proposed logging tool consists of three mutually orthogonal magnetic dipole sources and multiple three component magnetic field receivers. A sensitivity analysis indicates that the most important sensor configuration for providing 3D geological information about the borehole consists of a transmitter with moment aligned parallel to the axis of the borehole, and receivers aligned perpendicular to the axis. The standard coaxial logging configuration provides the greatest depth of sensitivity compared to other configurations, but offers no information regarding 3D structure. Two other tool configurations in which both the source and receiver are aligned perpendicular to the borehole axis provide some directional information and therefore better image resolution, but not true 3D information. A 3D inversion algorithm has been employed to demonstrate the plausibility of 3D inversion using data collected with the proposed logging tool. This study demonstrates that an increase in image resolution results when three orthogonal sources are incorporated into the logging tool rather than a single axially aligned source.

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

    PubMed

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-03-19

    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 3D-MIP platform when a larger number of cores is available. PMID:24910506

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

    PubMed Central

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-01-01

    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 3D-MIP platform when a larger number of cores is available. PMID:24910506

  3. Image-Based 3d Reconstruction and Analysis for Orthodontia

    NASA Astrophysics Data System (ADS)

    Knyaz, V. A.

    2012-08-01

    Among the main tasks of orthodontia are analysis of teeth arches and treatment planning for providing correct position for every tooth. The treatment plan is based on measurement of teeth parameters and designing perfect teeth arch curve which teeth are to create after treatment. The most common technique for teeth moving uses standard brackets which put on teeth and a wire of given shape which is clamped by these brackets for producing necessary forces to every tooth for moving it in given direction. The disadvantages of standard bracket technique are low accuracy of tooth dimensions measurements and problems with applying standard approach for wide variety of complex orthodontic cases. The image-based technique for orthodontic planning, treatment and documenting aimed at overcoming these disadvantages is proposed. The proposed approach provides performing accurate measurements of teeth parameters needed for adequate planning, designing correct teeth position and monitoring treatment process. The developed technique applies photogrammetric means for teeth arch 3D model generation, brackets position determination and teeth shifting analysis.

  4. 3D Reconstruction of virtual colon structures from colonoscopy images.

    PubMed

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

    2014-01-01

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

  5. 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.

  6. Molecular cloning, organization, expression and 3D structural analysis of the MHC class Ia gene in the whitespotted bamboo shark (Chiloscyllium plagiosum).

    PubMed

    Shen, Tong; Lei, Meiling; Wang, Jingru; He, Xiaoshun; Li, Xiuming; Li, Jianming

    2014-01-15

    Cartilaginous fishes are the oldest jawed vertebrates, from which the major histocompatibility complex (MHC) derived approximately 500 MYA; however, full-length genomic sequences for MHC genes in these species remain undescribed. This lack of basic information about MHC organization in cartilaginous fish is hindering investigations into the relationship between MHC polymorphism and disease, and leaves a large gap in our understanding of shark MHC evolution. Here, we obtained a complete 4887 bp genomic DNA of chplUAA (designated as chplUAA) from the whitespotted bamboo shark (Chiloscyllium plagiosum) using long PCR. The full-length cDNA sequence was 1385 bp, with a 1029 bp open reading frame (ORF) encoding 343 amino acids. Six unique sequences (chplUAA*01-06) were detected from 51 sequences from three samples. No more than two sequences were found in each individual, suggesting that only one UAA locus was amplified in each sample. Phylogenetic analysis supports monophyly of all available shark classical class Ia sequences. PMID:24315118

  7. Technical note: 3D representation and analysis of enthesis morphology.

    PubMed

    Noldner, Lara K; Edgar, Heather J H

    2013-11-01

    This comparison of methods for assessing the development of muscle insertion sites, or entheses, suggests that three-dimensional (3D) quantification of enthesis morphology can produce a picture of habitual muscle use patterns in a past population that is similar to one produced by ordinal scores for describing enthesis morphology. Upper limb skeletal elements (humeri, radii, and ulnae) from a sample of 24 middle-aged adult males from the Pottery Mound site in New Mexico were analyzed for both fibrous and fibrocartilaginous enthesis development with three different methods: ordinal scores, two-dimensional (2D) area measurements, and 3D surface areas. The methods were compared using tests for asymmetry and correlations among variables in each quantitative data set. 2D representations of enthesis area did not agree as closely as ordinal scores and 3D surface areas did regarding which entheses were significantly asymmetrical. There was significant correlation between 3D and 2D data, but correlation coefficients were not consistently high. Intraobserver error was also assessed for the 3D method. Cronbach's alpha values fell between 0.68 and 0.73, and error rates for all entheses fell between 10% and 15%. Marginally acceptable intraobserver error and the analytic versatility of 3D images encourage further investigation of using 3D scanning technology for quantifying enthesis development. PMID:24105032

  8. 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.

  9. Visualization and analysis of 3D gene expression patterns in zebrafish using web services

    NASA Astrophysics Data System (ADS)

    Potikanond, D.; Verbeek, F. J.

    2012-01-01

    The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and molecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with referenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a certain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an online visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in different developmental stages. We developed web services that provide programmable access to the 3D reconstruction data and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we develop a web application that uses these web services to retrieve data from our local information systems. The web application also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e. the ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the reconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative and spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain developmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be integrated in a web interface allowing the user to visualize the integrated information over the Internet.

  10. 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

  11. 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.

  12. 3D/1D Analysis of ICRF Antennas

    NASA Astrophysics Data System (ADS)

    Maggiora, Riccardo; Lancellotti, Vito; Vecchi, Giuseppe

    2003-10-01

    An innovative tool has been realized for the 3D/1D simulation of Ion Cyclotron Radio Frequency (ICRF), i.e. accounting for antennas in a realistic 3D geometry and with an accurate 1D plasma model. The approach to the problem is based on an integral-equation formulation for the self-consistent evaluation of the current distribution on the conductors. The environment has been subdivided in two coupled region: the plasma region and the vacuum region. The two problems are linked by means of a magnetic current (electric field) distribution on the aperture between the two regions. In the vacuum region all the calculations are executed in the spatial domain while in the plasma region an extraction in the spectral domain of some integrals is employed that permits to significantly reduce the integration support and to obtain a high numerical efficiency leading to the practical possibility of using a large number of sub-domain (rectangular or triangular) basis functions on each solid conductor of the system. The plasma enters the formalism of the plasma region via a surface impedance matrix; for this reason any plasma model can be used; at present the FELICE code has been adopted, that affords density and temperature profiles, and FLR effects. The source term directly models the TEM mode of the coax feeding the antenna and the current in the coax is determined self-consistently, giving the input impedance/admittance of the antenna itself. Calculation of field distributions (both magnetic and electric), useful for sheath considerations, is included. This tool has been implemented in a suite, called TOPICA, that is modular and applicable to ICRF antenna structures of arbitrary shape. This new simulation tool can assist during the detailed design phase and for this reason can be considered a "Virtual Prototyping Laboratory" (VPL). The TOPICA suite has been tested against assessed codes and against measurements and data of mock-ups and existing antennas. The VPL is being used in

  13. 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).

  14. 3D bicipital groove shape analysis and relationship to tendopathy.

    PubMed

    Ward, Aaron D; Hamarneh, Ghassan; Schweitzer, Mark E

    2008-06-01

    The bicipital groove of the proximal humerus is formed by the medial and lateral tuberosities and serves to retain the long biceps tendon in its proper place as the arm moves. Bicipital root and proximal tendon disorders are an important symptom generator in the shoulder. The accuracy of the diagnosis of many shoulder disorders visually without quantitative shape analysis is limited, motivating a clinical need for some ancillary method to assess the proximal biceps. In previous studies, measurements of bicipital groove shape were 2-dimensional (2D), taken from a single axial slice. Because of significant variations in groove shape from one axial slice to another in a single patient, such approaches risk overlooking shape features important to long biceps tendon pathology. In this paper, we present a study of the relationship between bicipital groove shape and long biceps tendon pathology using a novel 3-dimensional (3D) shape descriptor for the bicipital groove. In addition to providing quantitative measures of the shape of the groove and its relation to tendopathy, the new descriptor allows for intuitive, descriptive visualization of the shape of the groove. PMID:17342555

  15. Automatic 3-D grayscale volume matching and shape analysis.

    PubMed

    Guétat, Grégoire; Maitre, Matthieu; Joly, Laurène; Lai, Sen-Lin; Lee, Tzumin; Shinagawa, Yoshihisa

    2006-04-01

    Recently, shape matching in three dimensions (3-D) has been gaining importance in a wide variety of fields such as computer graphics, computer vision, medicine, and biology, with applications such as object recognition, medical diagnosis, and quantitative morphological analysis of biological operations. Automatic shape matching techniques developed in the field of computer graphics handle object surfaces, but ignore intensities of inner voxels. In biology and medical imaging, voxel intensities obtained by computed tomography (CT), magnetic resonance imagery (MRI), and confocal microscopes are important to determine point correspondences. Nevertheless, most biomedical volume matching techniques require human interactions, and automatic methods assume matched objects to have very similar shapes so as to avoid combinatorial explosions of point. This article is aimed at decreasing the gap between the two fields. The proposed method automatically finds dense point correspondences between two grayscale volumes; i.e., finds a correspondent in the second volume for every voxel in the first volume, based on the voxel intensities. Mutiresolutional pyramids are introduced to reduce computational load and handle highly plastic objects. We calculate the average shape of a set of similar objects and give a measure of plasticity to compare them. Matching results can also be used to generate intermediate volumes for morphing. We use various data to validate the effectiveness of our method: we calculate the average shape and plasticity of a set of fly brain cells, and we also match a human skull and an orangutan skull. PMID:16617625

  16. 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.

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

    PubMed

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

    2016-04-01

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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-02-01

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

  4. 3D Crustal Structure and 3D-b-value in AbuDabbab Seismogenic Source, Northern Red Sea.

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  5. 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

  6. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-07-01

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

  9. 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.

  10. 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.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Huang, T. S.

    1982-01-01

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

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  18. An unprecedented 3D POM-Ag architecture with intertwined and homological helical structures.

    PubMed

    Sha, Jing-Quan; Li, Meng-Ting; Sun, Jing-Wen; Zhang, Yu-Nan; Yan, Peng-Fei; Li, Guang-Ming

    2013-06-01

    A new hybrid compound, Na[Ag6(pyttz)2(H2O)][PMo12O40] (pyttz = 3-(pyrid-3-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl), has been hydrothermally synthesized and structurally characterized by routine techniques. X-ray diffraction analysis reveals that the title compound is constructed by the 2D Ag-pyttz coordination polymer and 3D Ag-POM architecture with helix. A fascinating structural feature is the assembling fashion of the right- and left-helical chain, namely, the helical chains with different orientations are intertwined with each other forming intertwined double helical layers along the c-axis, and the identical left- or right-handed helical chains are fused together in a hand-by-hand mode generating another homological helical layer along the a-axis. As a result, these helical layers intersect each other obtaining an unprecedented 3D POM-Ag inorganic architecture. Note that the 3D framework with a helix constructed by POMs and metal ions has never been observed up to date. Additionally, its photocatalytic degradation of RhB was also investigated. PMID:23558903

  19. 3D Thermoelectric Structures Derived from a New Mixed Micromachining Process

    NASA Astrophysics Data System (ADS)

    Du, Chen-Hsun; Lee, Chengkuo

    2000-12-01

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

  20. PACS-based interface for 3D anatomical structure visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Koehl, Christophe; Soler, Luc; Marescaux, Jacques

    2002-05-01

    The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

  1. Reconstruction of 3D structure using stochastic methods: morphology and transport properties

    NASA Astrophysics Data System (ADS)

    Karsanina, Marina; Gerke, Kirill; Čapek, Pavel; Vasilyev, Roman; Korost, Dmitry; Skvortsova, Elena

    2013-04-01

    One of the main factors defining numerous flow phenomena in rocks, soils and other porous media, including fluid and solute movements, is pore structure, e.g., pore sizes and their connectivity. Numerous numerical methods were developed to quantify single and multi-phase flow in such media on microscale. Among most popular ones are: 1) a wide range of finite difference/element/volume solutions of Navier-Stokes equations and its simplifications; 2) lattice-Boltzmann method; 3) pore-network models, among others. Each method has some advantages and shortcomings, so that different research teams usually utilize more than one, depending on the study case. Recent progress in 3D imaging of internal structure, e.g., X-ray tomography, FIB-SEM and confocal microscopy, made it possible to obtain digitized input pore parameters for such models, however, a trade-off between resolution and sample size is usually unavoidable. There are situations then only standard two-dimensional information of porous structure is known due to tomography high cost or resolution limitations. However, physical modeling on microscale requires 3D information. There are three main approaches to reconstruct (using 2D cut(s) or some other limited information/properties) porous media: 1) statistical methods (correlation functions and simulated annealing, multi-point statistics, entropy methods), 2) sequential methods (sphere or other granular packs) and 3) morphological methods. Stochastic reconstructions using correlation functions possess some important advantage - they provide a statistical description of the structure, which is known to have relationships with all physical properties. In addition, this method is more flexible for other applications to characterize porous media. Taking different 3D scans of natural and artificial porous materials (sandstones, soils, shales, ceramics) we choose some 2D cut/s as sources of input correlation functions. Based on different types of correlation functions

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

    PubMed

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

    2007-01-01

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

  3. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

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

  4. 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.

  5. 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

  6. 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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    2016-08-01

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

  10. Canonical structure of higher derivative gravity in 3D

    SciTech Connect

    Guellue, Ibrahim; Sisman, Tahsin Cagri; Tekin, Bayram

    2010-05-15

    We give an explicitly gauge-invariant canonical analysis of linearized quadratic gravity theories in three dimensions for both flat and de Sitter backgrounds. In flat backgrounds, we also study the effects of the gravitational Chern-Simons term, include the sources, and compute the weak field limit as well as scattering between spinning massive particles.

  11. 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.

  12. 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.

  13. 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.

  14. Texture analysis of the 3D collagen network and automatic classification of the physiology of articular cartilage.

    PubMed

    Duan, Xiaojuan; Wu, Jianping; Swift, Benjamin; Kirk, Thomas Brett

    2015-07-01

    A close relationship has been found between the 3D collagen structure and physiological condition of articular cartilage (AC). Studying the 3D collagen network in AC offers a way to determine the condition of the cartilage. However, traditional qualitative studies are time consuming and subjective. This study aims to develop a computer vision-based classifier to automatically determine the condition of AC tissue based on the structural characteristics of the collagen network. Texture analysis was applied to quantitatively characterise the 3D collagen structure in normal (International Cartilage Repair Society, ICRS, grade 0), aged (ICRS grade 1) and osteoarthritic cartilages (ICRS grade 2). Principle component techniques and linear discriminant analysis were then used to classify the microstructural characteristics of the 3D collagen meshwork and the condition of the AC. The 3D collagen meshwork in the three physiological condition groups displayed distinctive characteristics. Texture analysis indicated a significant difference in the mean texture parameters of the 3D collagen network between groups. The principle component and linear discriminant analysis of the texture data allowed for the development of a classifier for identifying the physiological status of the AC with an expected prediction error of 4.23%. An automatic image analysis classifier has been developed to predict the physiological condition of AC (from ICRS grade 0 to 2) based on texture data from the 3D collagen network in the tissue. PMID:24428581

  15. 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.

  16. 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

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

    SciTech Connect

    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.

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

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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).

  5. 3D Structured Grid Generation Codes for Turbomachinery

    NASA Technical Reports Server (NTRS)

    Loellbach, James; Tsung, Fu-Lin

    1999-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Yelkenci, Seda; Aktar, Mustafa

    2013-04-01

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

  7. 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

  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. Validation of 3D/1D Analysis of ICRF Antennas

    NASA Astrophysics Data System (ADS)

    Milanesio, D.; Lancellotti, V.; Kyrytsya, V.; Maggiora, R.; Vecchi, G.; Parisot, A.; Wukitch, S. J.

    2004-11-01

    An innovative tool has been realized for the 3D/1D simulation of Ion Cyclotron Radio Frequency (ICRF), i.e. accounting for antennas in a realistic 3D geometry and with an accurate 1D plasma model. The approach to the problem is based on an integral-equation formulation for the self-consistent evaluation of the current distribution on the conductors. The environment has been subdivided in two coupled region: the plasma region and the vacuum region. The two problems are linked by means of electromagnetic current distribution on the aperture between the two regions. The plasma enters the formalism via a surface impedance matrix for this reason any plasma model can be used. The source term directly models the TEM mode of the coax feeding the antenna and the current in the coax is determined self-consistently, giving the input impedance/admittance of the antenna itself. The suite, called TOPICA, has been used in the design of various ICRF antennas and also for the performance prediction of the ALCATOR C-MOD D and E antenna. An extensive set of comparisons between measured and simulated antenna parameters during ALCATOR C-MOD operation will be presented.

  10. 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.

  11. Measuring the impact of 3D data geometric modeling on spatial analysis: Illustration with Skyview factor

    NASA Astrophysics Data System (ADS)

    Brasebin, M.; Perret, J.; Mustière, S.; Weber, C.

    2012-10-01

    The increased availability of 3D urban data reflects a growing interest in 3D spatial analysis. As 3D spatial analysis often uses complex 3D data, studies of the potential gains of using more detailed 3D urban databases for specific uses is an important issue. First, more complex data implies an increase in time and memory usage for the analysis (and calls for more research on the efficiency of the algorithms used). Second, detailed 3D urban data are complex to produce, expensive and it is important to be well informed in order to decide whether of not to invest in such data. Currently, many studies have been led about the fitness for use of 2D data but they are very scarce concerning 3D data. This article presents a method to determine the influence of 3D modeling on the results of 3D analysis by isolating the potential sources of errors (such as roof modeling and geometric accuracy). This method is applied on two 3D datasets (LOD1 and LOD2) and a 3D indicator (the sky view factor or SVF). The results show that the significant influence of roof modeling is globally compensated by the difference in geometric modeling but that important local variations are noticed. Nevertheless, for 75% of the SVF processed the difference between the results using these two databases is lower than 2%.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  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. 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.

  19. 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.

  20. 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

  1. 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.

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

    PubMed

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

    2012-05-30

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

  3. 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.

  4. Error analysis of 3D laser scanning system for gangue monitoring

    NASA Astrophysics Data System (ADS)

    Hu, Shaoxing; Xia, Yuyang; Zhang, Aiwu

    2012-01-01

    The paper put forward the system error evaluation method of 3D scanning system for gangue monitoring; analyzed system errors including integrated error which can be avoided, and measurement error which needed whole analysis; firstly established the system equation after understanding the relationship of each structure. Then, used error independent effect and spread law to set up the entire error analysis system, and simulated the trend of error changing along X, Y, Z directions. At last, it is analytic that the laser rangefinder carries some weight in system error, and the horizontal and vertical scanning angles have some influences on system error in the certain vertical and horizontal scanning parameters.

  5. 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.

  6. 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

  7. 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. PMID:25121121

  8. 3D texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images

    NASA Astrophysics Data System (ADS)

    Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Khandelwal, Niranjan

    2013-02-01

    In this paper we have investigated a new approach for texture features extraction using co-occurrence matrix from volumetric lung CT image. Traditionally texture analysis is performed in 2D and is suitable for images collected from 2D imaging modality. The use of 3D imaging modalities provide the scope of texture analysis from 3D object and 3D texture feature are more realistic to represent 3D object. In this work, Haralick's texture features are extended in 3D and computed from volumetric data considering 26 neighbors. The optimal texture features to characterize the internal structure of Solitary Pulmonary Nodules (SPN) are selected based on area under curve (AUC) values of ROC curve and p values from 2-tailed Student's t-test. The selected texture feature in 3D to represent SPN can be used in efficient Computer Aided Diagnostic (CAD) design plays an important role in fast and accurate lung cancer screening. The reduced number of input features to the CAD system will decrease the computational time and classification errors caused by irrelevant features. In the present work, SPN are classified from Ground Glass Nodule (GGN) using Artificial Neural Network (ANN) classifier considering top five 3D texture features and top five 2D texture features separately. The classification is performed on 92 SPN and 25 GGN from Imaging Database Resources Initiative (IDRI) public database and classification accuracy using 3D texture features and 2D texture features provide 97.17% and 89.1% respectively.

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

    NASA Astrophysics Data System (ADS)

    Lemaître, Anaël

    2015-10-01

    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.

  10. Systematic error analysis for 3D nanoprofiler tracing normal vector

    NASA Astrophysics Data System (ADS)

    Kudo, Ryota; Tokuta, Yusuke; Nakano, Motohiro; Yamamura, Kazuya; Endo, Katsuyoshi

    2015-10-01

    In recent years, demand for an optical element having a high degree of freedom shape is increased. High-precision aspherical shape is required for the X-ray focusing mirror etc. For the head-mounted display etc., optical element of the free-form surface is used. For such an optical device fabrication, measurement technology is essential. We have developed a high- precision 3D nanoprofiler. By nanoprofiler, the normal vector information of the sample surface is obtained on the basis of the linearity of light. Normal vector information is differential value of the shape, it is possible to determine the shape by integrating. Repeatability of sub-nanometer has been achieved by nanoprofiler. To pursue the accuracy of shapes, systematic error is analyzed. The systematic errors are figure error of sample and assembly errors of the device. This method utilizes the information of the ideal shape of the sample, and the measurement point coordinates and normal vectors are calculated. However, measured figure is not the ideal shape by the effect of systematic errors. Therefore, the measurement point coordinate and the normal vector is calculated again by feeding back the measured figure. Correction of errors have been attempted by figure re-derivation. It was confirmed theoretically effectiveness by simulation. This approach also applies to the experiment, it was confirmed the possibility of about 4 nm PV figure correction in the employed sample.

  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. A quantitative analysis of 3-D coronary modeling from two or more projection images.

    PubMed

    Movassaghi, B; Rasche, V; Grass, M; Viergever, M A; Niessen, W J

    2004-12-01

    A method is introduced to examine the geometrical accuracy of the three-dimensional (3-D) representation of coronary arteries from multiple (two and more) calibrated two-dimensional (2-D) angiographic projections. When involving more then two projections, (multiprojection modeling) a novel procedure is presented that consists of fully automated centerline and width determination in all available projections based on the information provided by the semi-automated centerline detection in two initial calibrated projections. The accuracy of the 3-D coronary modeling approach is determined by a quantitative examination of the 3-D centerline point position and the 3-D cross sectional area of the reconstructed objects. The measurements are based on the analysis of calibrated phantom and calibrated coronary 2-D projection data. From this analysis a confidence region (alpha degrees approximately equal to [35 degrees - 145 degrees]) for the angular distance of two initial projection images is determined for which the modeling procedure is sufficiently accurate for the applied system. Within this angular border range the centerline position error is less then 0.8 mm, in terms of the Euclidean distance to a predefined ground truth. When involving more projections using our new procedure, experiments show that when the initial pair of projection images has an angular distance in the range alpha degrees approximately equal to [35 degrees - 145 degrees], the centerlines in all other projections (gamma = 0 degrees - 180 degrees) were indicated very precisely without any additional centering procedure. When involving additional projection images in the modeling procedure a more realistic shape of the structure can be provided. In case of the concave segment, however, the involvement of multiple projections does not necessarily provide a more realistic shape of the reconstructed structure. PMID:15575409

  13. 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

  14. 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.

  15. 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

  16. 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

  17. A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis.

    PubMed

    Xu, Yiwen; Pickering, J Geoffrey; Nong, Zengxuan; Gibson, Eli; Arpino, John-Michael; Yin, Hao; Ward, Aaron D

    2015-01-01

    Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision) were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error), as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections). Accumulated error measures were lower (p < 0.01) for the nucleus landmark technique and superior vasculature continuity was observed. These findings indicate that registration based on automatic extraction and correspondence of small, homologous landmarks may support accurate 3D histology reconstruction. This technique avoids the otherwise problematic "banana-into-cylinder" effect observed using conventional methods that optimize the pairwise alignment of salient structures, forcing them to be section-orthogonal. This approach will provide a valuable tool for high-accuracy 3D histology tissue reconstructions for

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

    PubMed

    Zhang, Fengxiang; Low, Hong Yee

    2008-10-15

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

  19. Microstructure analysis of the secondary pulmonary lobules by 3D synchrotron radiation CT

    NASA Astrophysics Data System (ADS)

    Fukuoka, Y.; Kawata, Y.; Niki, N.; Umetani, K.; Nakano, Y.; Ohmatsu, H.; Moriyama, N.; Itoh, H.

    2014-03-01

    Recognition of abnormalities related to the lobular anatomy has become increasingly important in the diagnosis and differential diagnosis of lung abnormalities at clinical routines of CT examinations. This paper aims a 3-D microstructural analysis of the pulmonary acinus with isotropic spatial resolution in the range of several micrometers by using micro CT. Previously, we demonstrated the ability of synchrotron radiation micro CT (SRμCT) using offset scan mode in microstructural analysis of the whole part of the secondary pulmonary lobule. In this paper, we present a semiautomatic method to segment the acinar and subacinar airspaces from the secondary pulmonary lobule and to track small vessels running inside alveolar walls in human acinus imaged by the SRμCT. The method beains with and segmentation of the tissues such as pleural surface, interlobular septa, alveola wall, or vessel using a threshold technique and 3-D connected component analysis. 3-D air space are then conustructed separated by tissues and represented branching patterns of airways and airspaces distal to the terminal bronchiole. A graph-partitioning approach isolated acini whose stems are interactively defined as the terminal bronchiole in the secondary pulmonary lobule. Finally, we performed vessel tracking using a non-linear sate space which captures both smoothness of the trajectories and intensity coherence along vessel orientations. Results demonstrate that the proposed method can extract several acinar airspaces from the 3-D SRμCT image of secondary pulmonary lobule and that the extracted acinar airspace enable an accurate quantitative description of the anatomy of the human acinus for interpretation of the basic unit of pulmonary structure and function.

  20. Shadow Effect on Photovoltaic Potentiality Analysis Using 3d City Models

    NASA Astrophysics Data System (ADS)

    Alam, N.; Coors, V.; Zlatanova, S.; Oosterom, P. J. M.

    2012-07-01

    Due to global warming, green-house effect and various other drawbacks of existing energy sources, renewable energy like Photovoltaic system is being popular for energy production. The result of photovoltaic potentiality analysis depends on data quality and parameters. Shadow rapidly decreases performance of the Photovoltaic system and it always changes due to the movement of the sun. Solar radiation incident on earth's atmosphere is relatively constant but the radiation at earth's surface varies due to absorption, scattering, reflection, change in spectral content, diffuse component, water vapor, clouds and pollution etc. In this research, it is being investigated that how efficiently real-time shadow can be detected for both direct and diffuse radiation considering reflection and other factors in contrast with the existing shadow detection methods using latest technologies and what is the minimum quality of data required for this purpose. Of course, geometric details of the building geometry and surroundings directly affect the calculation of shadows. In principle, 3D city models or point clouds, which contain roof structure, vegetation, thematically differentiated surface and texture, are suitable to simulate exact real-time shadow. This research would develop an automated procedure to measure exact shadow effect from the 3D city models and a long-term simulation model to determine the produced energy from the photovoltaic system. In this paper, a developed method for detecting shadow for direct radiation has been discussed with its result using a 3D city model to perform a solar energy potentiality analysis.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    PubMed

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2008-08-10

    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 FSI

  9. 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

  10. and 3D TOF-SIMS Imaging for Biological Analysis

    NASA Astrophysics Data System (ADS)

    Fletcher, John S.

    Secondary ion mass spectrometry (SIMS) is an established technique in the field of surface analysis but until recently has played only a very small role in the area of biological analysis. This chapter provides an overview of the application of secondary ion mass spectrometry to the analysis of biological samples including single cells, bacteria and tissue sections. The chapter will discuss how the challenges of biological analysis by SIMS have created an impetus for the development of new technology and methodology giving improved mass resolution, spatial resolution and sensitivity.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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%.

  19. 3D distribution of interstellar medium in the Galaxy: Preparation for analysis of Gaia observations

    NASA Astrophysics Data System (ADS)

    Puspitarini, Lucky; Lallement, Rosine

    2015-09-01

    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.

  20. 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.

  1. Diagnostic clinical benefits of digital spot and digital 3D mammography following analysis of screening findings

    NASA Astrophysics Data System (ADS)

    Lehtimaki, Mari; Pamilo, Martti; Raulisto, Leena; Roiha, Marja; Kalke, Martti; Siltanen, Samuli; Ihamäki, Timo

    2003-05-01

    The purpose of this study is to find out the impact of 3-dimensional digital mammography and digital spot imaging following analysis of the abnormal findings of screening mammograms. Over a period of eight months, digital 3-D mammography imaging TACT Tuned Aperture Computed Tomography+, digital spot imaging (DSI), screen-film mammography imaging (SFM) and diagnostic film imaging (DFM) examinations were performed on 60 symptomatic cases. All patients were recalled because it was not possible to exclude the presence of breast cancer on screening films. Abnormal findings on the screening films were non-specific tumor-like parenchymal densities, parenchymal asymmetries or distortions with or without microcalcifications or just microcalcifications. Mammography work-up (film imaging) included spot compression and microfocus magnification views. The 3-D softcopy reading in all cases was done with Delta 32 TACT mammography workstation, while the film images were read using a mammography-specific light box. During the softcopy reading only windowing tools were allowed. The result of this study indicates that the clinical diagnostic image quality of digital 3-D and digital spot images are better than in film images, even in comparison with diagnostic work-up films. Potential advantages are to define if the mammography finding is caused by a real abnormal lesion or by superimposition of normal parenchymal structures, to detect changes in breast tissue which would otherwise be missed, to verify the correct target for biopsies and to reduce the number of biopsies performed.

  2. 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.

  3. 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.

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

    PubMed

    Sillitoe, Ian; Lewis, Tony; Orengo, Christine

    2015-01-01

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

  5. 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.

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

    PubMed

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

    2016-04-28

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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Rigid bodies for metal forming analysis with NIKE3D

    SciTech Connect

    Maker, B.N.

    1995-01-25

    Perhaps the most common approximation in engineering is that, relative to its neighbors, a system component is structurally rigid. This paper presents a development of the rigid assumption for use in nonlinear, implicit finite element codes. In this method, computational economy is gained by condensing the size of the associated linear system of equations, eliminating the processing of rigid elements, and reducing the overall nonlinearity of the problem.

  12. 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.

  13. 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.

  14. 3D neutronic/thermal-hydraulic coupled analysis of MYRRHA

    SciTech Connect

    Vazquez, M.; Martin-Fuertes, F.

    2012-07-01

    The current tendency in multiphysics calculations applied to reactor physics is the use of already validated computer codes, coupled by means of an iterative approach. In this paper such an approach is explained concerning neutronics and thermal-hydraulics coupled analysis with MCNPX and COBRA-IV codes using a driver program and file exchange between codes. MCNPX provides the neutronic analysis of heterogeneous nuclear systems, both in critical and subcritical states, while COBRA-IV is a subchannel code that can be used for rod bundles or core thermal-hydraulics analysis. In our model, the MCNP temperature dependence of nuclear data is handled via pseudo-material approach, mixing pre-generated cross section data set to obtain the material with the desired cross section temperature. On the other hand, COBRA-IV has been updated to allow for the simulation of liquid metal cooled reactors. The coupled computational tool can be applied to any geometry and coolant, as it is the case of single fuel assembly, at pin-by-pin level, or full core simulation with the average pin of each fuel-assembly. The coupling tool has been applied to the critical core layout of the SCK-CEN MYRRHA concept, an experimental LBE cooled fast reactor presently in engineering design stage. (authors)

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

    PubMed Central

    Bhattacharya, Debswapna; Cheng, Jianlin

    2013-01-01

    Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8th CASP experiment. During the 9th and recently concluded 10th CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as ‘MULTICOM-CONSTRUCT’) was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine is freely available at http://protein.rnet.missouri.edu/i3drefine/. PMID:23894517

  2. 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.

  3. 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.

  4. 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.

  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. 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. PMID:25451822

  7. 3-D stress analysis in laminated plates using a combination of ANSYS and sub-element/deficient approximation function analysis

    SciTech Connect

    Bogdanovich, A.; Pastore, C.; Kumar, V.; German, M.

    1994-12-31

    The method of combining the use of ANSYS SOLID 46 finite element and the sub-element/deficient approximation function (SEDAF) analysis is developed and demonstrated on the benchmark problem of Pagano. The algorithm incorporates a primary displacement calculation using ANSYS and the successive stress calculation using 3-D SEDAF analysis. A special mathematical procedure aimed to convert the global displacement output of the commercial finite element code into the local displacement input of the SEDAF analysis is presented. The results show a considerably higher accuracy provided by this combination compared to the original ANSYS results when calculating both the in-plane and transverse stresses, especially for their values at the interfaces. After some generalization, the presented ANSYS/SEDAF algorithm seems to be promising for obtaining a sufficiently accurate 3-D stress distributions in any structural analysis problem allowing for the application of ANSYS code.

  8. 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

  9. 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

  10. Sexual Dimorphism Analysis and Gender Classification in 3D Human Face

    NASA Astrophysics Data System (ADS)

    Hu, Yuan; Lu, Li; Yan, Jingqi; Liu, Zhi; Shi, Pengfei

    In this paper, we present the sexual dimorphism analysis in 3D human face and perform gender classification based on the result of sexual dimorphism analysis. Four types of features are extracted from a 3D human-face image. By using statistical methods, the existence of sexual dimorphism is demonstrated in 3D human face based on these features. The contributions of each feature to sexual dimorphism are quantified according to a novel criterion. The best gender classification rate is 94% by using SVMs and Matcher Weighting fusion method.This research adds to the knowledge of 3D faces in sexual dimorphism and affords a foundation that could be used to distinguish between male and female in 3D faces.

  11. Photoemission spectroscopy and X-ray diffraction analysis of 3D topological and Kondo insulators

    NASA Astrophysics Data System (ADS)

    Shibayev, Pavel

    2015-03-01

    The advantage of studying 3D topological insulators (TIs), compounds that have attracted the attention of many in the condensed matter field, is the ability for their existence at room temperature and no magnetic fields, allowing both for resolving their band structure via angle-resolved photoemission spectroscopy (ARPES) and understanding electrical transport and other properties via X-ray diffraction (XRD) and point-contact spectroscopy (PCS). A comprehensive quantitative analysis of Bi2Se3, a 3D TI, was carried out using these methods. The Bi2Se3\\ crystals were synthesized in-house at Princeton University. A first-principles calculation based on density functional theory, DFT, was performed using the Abinit software. The band structure of the crystal was then resolved via ARPES at the Advanced Light Source in LBNL, resulting in a surprisingly stark and clear single Dirac cone. A large band gap was confirmed, suggesting an increased potential for applications. In contrast, Kondo insulators are found in rare-earth based materials with f-electron degrees of freedom. Photon energy dependent dispersion relationships and temperature dependence studies were performed on a Kondo candidate CeB6 via ARPES, showing an even number of Dirac cones and a non-TI behavior. Analysis of I-V characteristics through PCS will follow, in addition to characterization via Bruker XRD for both compounds. Research group led by Professor M. Zahid Hasan (Princeton University).

  12. 2D and 3D X-Ray Structural Microscopy Using Submicron-Resolution Laue Microdiffraction

    SciTech Connect

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

    2010-11-10

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

  13. 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.

  14. Image-based 3D scene analysis for navigation of autonomous airborne systems

    NASA Astrophysics Data System (ADS)

    Jaeger, Klaus; Bers, Karl-Heinz

    2001-10-01

    In this paper we describe a method for automatic determination of sensor pose (position and orientation) related to a 3D landmark or scene model. The method is based on geometrical matching of 2D image structures with projected elements of the associated 3D model. For structural image analysis and scene interpretation, a blackboard-based production system is used resulting in a symbolic description of image data. Knowledge of the approximated sensor pose measured for example by IMU or GPS enables to estimate an expected model projection used for solving the correspondence problem of image structures and model elements. These correspondences are presupposed for pose computation carried out by nonlinear numerical optimization algorithms. We demonstrate the efficiency of the proposed method by navigation update approaching a bridge scenario and flying over urban area, whereas data were taken with airborne infrared sensors in high oblique view. In doing so we simulated image-based navigation for target engagement and midcourse guidance suited for the concepts of future autonomous systems like missiles and drones.

  15. Tunneling Analyst: A 3D GIS extension for rock mass classification and fault zone analysis in tunneling

    NASA Astrophysics Data System (ADS)

    Choi, Yosoon; Yoon, Seo-Youn; Park, Hyeong-Dong

    2009-06-01

    In this study, an extension called Tunneling Analyst (TA) has been developed in ArcScene 3D GIS software, part of the ArcGIS software package. It dramatically extends the functionalities of ArcScene because it allows: (1) estimation of the 3D distribution of rock mass rating (RMR) values using borehole and geophysical exploration data, (2) the modeling of 3D discontinuity planes such as faults from field-based structural measurements, and (3) analysis of 3D intersections and 3D buffer zones between proposed tunnel alignments and some discontinuities. Because TA can handle and visualize both 2D and 3D geological data in a single GIS environment, the tedious tasks required for data conversion between various software packages can be reduced significantly. The application to the Daecheong tunneling project in Korea shows that TA could present a rational solution to evaluating the rock mass classes along a proposed tunnel alignment and can also provide specific 3D spatial query tools to support the tunnel design work. This paper describes the concept and details of the development and implementation of TA.

  16. Function and 3D Structure of the N-Glycans on Glycoproteins

    PubMed Central

    Nagae, Masamichi; Yamaguchi, Yoshiki

    2012-01-01

    Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of “snapshots” of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as “molecular glue” to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site. PMID:22942711

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed Central

    Esquivel-Rodríguez, Juan; Kihara, Daisuke

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    While outstanding functional properties of thin NiTi wires are nowadays well recognized and beneficially utilized in medical NiTi devices, development of 2D/3D wire structures made out of these NiTi wires remains challenging and mostly unexplored. The research is driven by the idea of creating novel 2D/3D smart structures which inherit the functional properties of NiTi wires and actively utilize geometrical deformations within the structure to create new/improved functional properties. Generally, textile technology provides attractive processing methods for manufacturing 2D/3D smart structures made out of NiTi wires. Such structures may be beneficially combined with soft elastomers to create smart deformable composites. Following this route, we carried out experimental work focused on development of 3D flexible NiTi-braided elastomer composites involving their design, laboratory manufacture and thermomechanical testing. We describe the manufacturing technology and structural properties of these composites; and perform thermomechanical tests on the composites, focusing particularly on quasistatic tensile properties, energy absorption, damping and actuation under tensile loading. Functional thermomechanical properties of the composites are discussed with regard to the mechanical properties of the components and architecture of the composites. It is found that the composites indeed inherit all important features of the thermomechanical behavior of NiTi wires but, due to their internal architecture, outperform single NiTi wires in some features such as the magnitude of recoverable strain, superelastic damping capacity and thermally induced actuation strain.

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

    PubMed

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

    2016-07-01

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

  2. 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.

  3. 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

  4. 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

  5. Pore-scale intermittent velocity structure underpinning anomalous transport through 3-D porous media

    NASA Astrophysics Data System (ADS)

    Kang, Peter K.; Anna, Pietro; Nunes, Joao P.; Bijeljic, Branko; Blunt, Martin J.; Juanes, Ruben

    2014-09-01

    We study the nature of non-Fickian particle transport in 3-D porous media by simulating fluid flow in the intricate pore space of real rock. We solve the full Navier-Stokes equations at the same resolution as the 3-D micro-CT (computed tomography) image of the rock sample and simulate particle transport along the streamlines of the velocity field. We find that transport at the pore scale is markedly anomalous: longitudinal spreading is superdiffusive, while transverse spreading is subdiffusive. We demonstrate that this anomalous behavior originates from the intermittent structure of the velocity field at the pore scale, which in turn emanates from the interplay between velocity heterogeneity and velocity correlation. Finally, we propose a continuous time random walk model that honors this intermittent structure at the pore scale and captures the anomalous 3-D transport behavior at the macroscale.

  6. Element-specific X-ray phase tomography of 3D structures at the nanoscale.

    PubMed

    Donnelly, Claire; Guizar-Sicairos, Manuel; Scagnoli, Valerio; Holler, Mirko; Huthwelker, Thomas; Menzel, Andreas; Vartiainen, Ismo; Müller, Elisabeth; Kirk, Eugenie; Gliga, Sebastian; Raabe, Jörg; Heyderman, Laura J

    2015-03-20

    Recent advances in fabrication techniques to create mesoscopic 3D structures have led to significant developments in a variety of fields including biology, photonics, and magnetism. Further progress in these areas benefits from their full quantitative and structural characterization. We present resonant ptychographic tomography, combining quantitative hard x-ray phase imaging and resonant elastic scattering to achieve ab initio element-specific 3D characterization of a cobalt-coated artificial buckyball polymer scaffold at the nanoscale. By performing ptychographic x-ray tomography at and far from the Co K edge, we are able to locate and quantify the Co layer in our sample to a 3D spatial resolution of 25 nm. With a quantitative determination of the electron density we can determine that the Co layer is oxidized, which is confirmed with microfluorescence experiments. PMID:25839287

  7. 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.

  8. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  9. 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.

  10. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

    PubMed Central

    Huang, Yan Xin; Bao, Yong Li; Guo, Shu Yan; Wang, Yan; Zhou, Chun Guang; Li, Yu Xin

    2008-01-01

    Background The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues of interaction between an antigen and an antibody. Consequently, this area of research has received considerable attention from immunologists, structural biologists and computational biologists. Phage-displayed random peptide libraries are powerful tools used to obtain mimotopes that are selected by binding to a given monoclonal antibody (mAb) in a similar way to the native epitope. These mimotopes can be considered as functional epitope mimics. Mimotope analysis based methods can predict not only linear but also conformational epitopes and this has been the focus of much research in recent years. Though some algorithms based on mimotope analysis have been proposed, the precise localization of the interaction site mimicked by the mimotopes is still a challenging task. Results In this study, we propose a method for B-cell epitope prediction based on mimotope analysis called Pep-3D-Search. Given the 3D structure of an antigen and a set of mimotopes (or a motif sequence derived from the set of mimotopes), Pep-3D-Search can be used in two modes: mimotope or motif. To evaluate the performance of Pep-3D-Search to predict epitopes from a set of mimotopes, 10 epitopes defined by crystallography were compared with the predicted results from a Pep-3D-Search: the average Matthews correlation oefficient (MCC), sensitivity and precision were 0.1758, 0.3642 and 0.6948. Compared with other available prediction algorithms, Pep-3D-Search showed comparable MCC, specificity and precision, and could provide novel, rational results. To verify the capability of Pep-3D-Search to align a motif sequence to a 3D structure for predicting epitopes, 6 test cases were used. The predictive performance of Pep-3D-Search was demonstrated to be superior to that of other

  11. 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.

  12. 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

    2010-01-01

    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. PMID:21124830

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Fabrication and characterization of metal-to-metal interconnect structures for 3-D integration

    NASA Astrophysics Data System (ADS)

    Huffman, Alan; Lannon, John; Lueck, Matthew; Gregory, Christopher; Temple, Dorota

    2009-03-01

    The use of collapsible (solder) bump interconnects in pixel detector hybridization has been shown to be very successful. However, as pixel sizes decrease, the use of non-collapsible metal-to-metal bump bonding methods is needed to push the interconnect dimensions smaller. Furthermore, these interconnects are compatible with 3D intgration technologies which are being considered to increase overall pixel and system performance. These metal-to-metal bonding structures provide robust mechanical and electrical connections and allow for a dramatic increase in pixel density. Of particular interest are Cu-Cu thermocompression bonding and Cu/Sn-Cu solid-liquid diffusion bonding processes. Working with Fermilab, RTI undertook a demonstration to show that these bump structures could be reliably used to interconnect devices designed with 20 micron I/O pitch. Cu and Cu/Sn bump fabrication processes were developed to provide a well-controlled surface topography necessary for the formation of low resistance, high yielding, and reliable interconnects. The electrical resistance and yield has been quantified based on electrical measurements of daisy chain test structures and the mechanical strength of the bonding has been quantified through die shear testing. The reliability has been characterized through studies of the impact of thermal exposure on the mechanical performance of the bonds. Cross-section SEM analysis, coupled with high resolution energy dispersive spectroscopy, has provided insight into the physical and chemical nature of the bonding interfaces and aided in the evaluation of the long-term stability of the bonds.

  20. What spherically symmetric viscosity structure produces the same PGR as a realistic 3D Earth?

    NASA Astrophysics Data System (ADS)

    Paulson, A.; Zhong, S.; Wahr, J.

    2003-04-01

    Observations of isostatic adjustment of the earth's surface due to transient loading provide important constraints on the mantle viscosity structure. However, most studies of this response have assumed a spherically symmetric (1D) earth. This study is motivated by the following question: when a one-dimensional viscosity model is derived from post-glacial rebound (PGR) observations, how does this 1D structure correspond to the three-dimensional structure of the earth? Using the 3D spherical finite element software CitcomSVE [Zhong et al., 2002], we are able to compute the earth's response to realistic glacial loading when the earth has a truly 3D viscosity structure. The loading is provided by the ICE-3G deglaciation history [Tushingham &Peltier, 1991]. The 3D viscosity structure is constructed by first selecting a priori a radial average viscosity (for example, ( 1021 \\: {Pa \\cdot s}) in the upper mantle and (2 × 1021 \\: {Pa \\cdot s}) in the lower mantle). The lateral variations about this radial structure are derived from seismic shear-velocity tomography models by converting velocities to temperature, then temperature to viscosity. The seismic tomography models used are S20RTS [Ritsema et al., 1999] and NA00 [Van der Lee, 2002]. From the computed isostatic response, we measure typical PGR observables: relative sea level change (RSLC) and (dot{J2}). These measurements are then treated as synthetic data, and we search for 1D (radially stratified) viscosity models, forced with the same glaciation history, that will best fit these synthetic PGR observations. We find that for sites near the center of a large glacial load (e.g., southern Hudson Bay), a local average of the 3D viscosity structure provides a reasonable 1D proxy. For sites along the periphery of the glacial load (e.g., Boston), it is much more difficult to find a 1D model that can reproduce the 3D observations. We also approach the problem by running an ensemble of 1D viscosity models, and finding

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

    NASA Astrophysics Data System (ADS)

    Zhang, Zhi-Dong

    2013-03-01

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

  2. 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…

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

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

    Muench, Thomas; Koch, Manfred; Schlittenhardt, Jörg

    2010-05-01

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

  13. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells

    PubMed Central

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L.; Han, Jessica H.; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H.; Bussey, Kimberly J.; Meldrum, Deirdre R.

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an ‘epigenetic’ drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat’s differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  14. Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

    PubMed

    Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

    2016-01-01

    The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action. PMID:27503568

  15. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures.

    PubMed

    Zenou, M; Sa'ar, A; Kotler, Z

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  16. Laser jetting of femto-liter metal droplets for high resolution 3D printed structures

    PubMed Central

    Zenou, M.; Sa’ar, A.; Kotler, Z.

    2015-01-01

    Laser induced forward transfer (LIFT) is employed in a special, high accuracy jetting regime, by adequately matching the sub-nanosecond pulse duration to the metal donor layer thickness. Under such conditions, an effective solid nozzle is formed, providing stability and directionality to the femto-liter droplets which are printed from a large gap in excess of 400 μm. We illustrate the wide applicability of this method by printing several 3D metal objects. First, very high aspect ratio (A/R > 20), micron scale, copper pillars in various configuration, upright and arbitrarily bent, then a micron scale 3D object composed of gold and copper. Such a digital printing method could serve the generation of complex, multi-material, micron-scale, 3D materials and novel structures. PMID:26602432

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  1. 3D shape analysis for early diagnosis of malignant lung nodules.

    PubMed

    El-Baz, Ayman; Nitzken, Matthew; Elnakib, Ahmed; Khalifa, Fahmi; Gimel'farb, Georgy; Falk, Robert; El-Ghar, Mohamed Abou

    2011-01-01

    An alternative method of diagnosing malignant lung nodules by their shape, rather than conventional growth rate, is proposed. The 3D surfaces of the detected lung nodules are delineated by spherical harmonic analysis that represents a 3D surface of the lung nodule supported by the unit sphere with a linear combination of special basis functions, called Spherical Harmonics (SHs). The proposed 3D shape analysis is carried out in five steps: (i) 3D lung nodule segmentation with a deformable 3D boundary controlled by a new prior visual appearance model; (ii) 3D Delaunay triangulation to construct a 3D mesh model of the segmented lung nodule surface; (iii) mapping this model to the unit sphere; (iv) computing the SHs for the surface; and (v) determining the number of the SHs to delineate the lung nodule. We describe the lung nodule shape complexity with a new shape index, the estimated number of the SHs, and use it for the K-nearest classification into malignant and benign lung nodules. Preliminary experiments on 327 lung nodules (153 malignant and 174 benign) resulted in a classification accuracy of 93.6%, showing that the proposed method is a promising supplement to current technologies for the early diagnosis of lung cancer. PMID:22003697

  2. 3D shape analysis for early diagnosis of malignant lung nodules.

    PubMed

    El-Bazl, Ayman; Nitzken, Matthew; Khalifa, Fahmi; Elnakib, Ahmed; Gimel'farb, Georgy; Falk, Robert; El-Ghar, Mohammed Abo

    2011-01-01

    An alternative method for diagnosing malignant lung nodules by their shape rather than conventional growth rate is proposed. The 3D surfaces of the detected lung nodules are delineated by spherical harmonic analysis, which represents a 3D surface of the lung nodule supported by the unit sphere with a linear combination of special basis functions, called spherical harmonics (SHs). The proposed 3D shape analysis is carried out in five steps: (i) 3D lung nodule segmentation with a deformable 3D boundary controlled by two probabilistic visual appearance models (the learned prior and the estimated current appearance one); (ii) 3D Delaunay triangulation to construct a 3D mesh model of the segmented lung nodule surface; (iii) mapping this model to the unit sphere; (iv) computing the SHs for the surface, and (v) determining the number of the SHs to delineate the lung nodule. We describe the lung nodule shape complexity with a new shape index, the estimated number of the SHs, and use it for the K-nearest classification to distinguish malignant and benign lung nodules. Preliminary experiments on 327 lung nodules (153 malignant and 174 benign) resulted in the 93.6% correct classification (for the 95% confidence interval), showing that the proposed method is a promising supplement to current technologies for the early diagnosis of lung cancer. PMID:21761703

  3. 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…

  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. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. 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

  14. Novel 3D Microscopic Analysis of Human Placental Villous Trees Reveals Unexpected Significance of Branching Angles

    PubMed Central

    Haeussner, Eva; Buehlmeyer, Antonia; Schmitz, Christoph; von Koch, Franz Edler; Frank, Hans-Georg

    2014-01-01

    The villous trees of human placentas delineate the fetomaternal border and are complex three-dimensional (3D) structures. Thus far, they have primarily been analyzed as thin, two-dimensional (2D) histological sections. However, 2D sections cannot provide access to key aspects such as branching nodes and branch order. Using samples taken from 50 normal human placentas at birth, in the present study we show that analysis procedures for 3D reconstruction of neuronal dendritic trees can also be used for analyzing trees of human placentas. Nodes and their branches (e.g., branching hierarchy, branching angles, diameters, and lengths of branches) can be efficiently measured in whole-mount preparations of isolated villous trees using high-end light microscopy. Such data differ qualitatively from the data obtainable from histological sections and go substantially beyond the morphological horizon of such histological data. Unexpectedly, branching angles of terminal branches of villous trees varied inversely with the fetoplacental weight ratio, a widely used clinical parameter. Since branching angles have never before been determined in the human placenta, this result requires further detailed studies in order to fully understand its impact. PMID:25155961

  15. 3D photography in the objective analysis of volume augmentation including fat augmentation and dermal fillers.

    PubMed

    Meier, Jason D; Glasgold, Robert A; Glasgold, Mark J

    2011-11-01

    The authors present quantitative and objective 3D data from their studies showing long-term results with facial volume augmentation. The first study analyzes fat grafting of the midface and the second study presents augmentation of the tear trough with hyaluronic filler. Surgeons using 3D quantitative analysis can learn the duration of results and the optimal amount to inject, as well as showing patients results that are not demonstrable with standard, 2D photography. PMID:22004863

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

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

    NASA Astrophysics Data System (ADS)

    Lee, M. C.; Tsai, Y. L.; Wang, R. Z.; Lin, M. L.

    2015-08-01

    Heritage buildings are highly prone to long term damage from the microclimate, scourge and vandalism, which can result in damaged materials, structures, painting and cultural heritage items. This study will focus on finding the displacement of wood structural members through the use of a 3D laser scanner and the 4D concept of time. The results will compare the scans from different periods to find the difference (if any) in the structural member position. Wood structures usually consist of numerous wood members connected to form the structure. However, these members can be damaged in various ways such as physical mechanisms, chemical reactions, and biological corrosion. When damage to the wood structure occurs, the structural displacement can be affected, and if affected severely, can lead to a building collapse. Monitoring of the structural displacement is the best way to discover damage immediately and to preserve the heritage building. However, the Cultural Heritage Preservation Law in Taiwan prohibits the installation of monitoring instruments (e.g strain gauge, accelerometer) in historic structures (heritage buildings). Scanning the wood structure with 3D lasers is the most non-intrusive method and quickly achieves displacement through visualization. The displacement scan results can be compared with different periods and different members to analyze the severity of damage. Once the 3D scanner is installed, the whole building is scanned, and point clouds created to build the visual building model. The structural displacement can be checked via the building model and the differences are measured between each member to find the high risk damaged areas or members with large displacement. Early detection of structural damage is the most effective way means of preservation.

  6. Application of FUN3D and CFL3D to the Third Workshop on CFD Uncertainty Analysis

    NASA Technical Reports Server (NTRS)

    Rumsey, C. L.; Thomas, J. L.

    2008-01-01

    Two Reynolds-averaged Navier-Stokes computer codes - one unstructured and one structured - are applied to two workshop cases (for the 3rd Workshop on CFD Uncertainty Analysis, held at Instituto Superior Tecnico, Lisbon, in October 2008) for the purpose of uncertainty analysis. The Spalart-Allmaras turbulence model is employed. The first case uses the method of manufactured solution and is intended as a verification case. In other words, the CFD solution is expected to approach the exact solution as the grid is refined. The second case is a validation case (comparison against experiment), for which modeling errors inherent in the turbulence model and errors/uncertainty in the experiment may prevent close agreement. The results from the two computer codes are also compared. This exercise verifies that the codes are consistent both with the exact manufactured solution and with each other. In terms of order property, both codes behave as expected for the manufactured solution. For the backward facing step, CFD uncertainty on the finest grid is computed and is generally very low for both codes (whose results are nearly identical). Agreement with experiment is good at some locations for particular variables, but there are also many areas where the CFD and experimental uncertainties do not overlap.

  7. Analysis of Composite Panel-Stiffener Debonding Using a Shell/3D Modeling Technique

    NASA Technical Reports Server (NTRS)

    Krueger, Ronald; Minguet, Pierre J.

    2006-01-01

    Interlaminar fracture mechanics has proven useful for characterizing the onset of delaminations in composites and has been used with limited success primarily to investigate onset in fracture toughness specimens and laboratory size coupon type specimens. Future acceptance of the methodology by industry and certification authorities however, requires the successful demonstration of the methodology on structural level. For this purpose a panel was selected that was reinforced with stringers. Shear loading cases the panel to buckle and the resulting out-of-plane deformations initiate skin/stringer separation at the location of an embedded defect. For finite element analysis, the panel and surrounding load fixture were modeled with shell element. A small section of the stringer foot and the panel in the vicinity of the embedded defect were modeled with a local 3D solid model. A failure index was calculated by correlating computed mixed-mode failure criterion of the graphite/epoxy material.

  8. A Shell/3D Modeling Technique for the Analysis of Delaminated Composite Laminates

    NASA Technical Reports Server (NTRS)

    Krueger, Ronald; OBrien, T. Kevin

    2000-01-01

    A shell/3D modeling technique was developed for which a local solid finite element model is used only in the immediate vicinity of the delamination front. The goal was to combine the accuracy of the full three-dimensional solution with the computational efficiency of a shell finite element model. Multi-point constraints provided a kinematically compatible interface between the local 3D model and the global structural model which has been meshed with shell finite elements. Double Cantilever Beam, End Notched Flexure, and Single Leg Bending specimens were analyzed first using full 3D finite element models to obtain reference solutions. Mixed mode strain energy release rate distributions were computed using the virtual crack closure technique. The analyses were repeated using the shell/3D technique to study the feasibility for pure mode I, mode II and mixed mode I/II cases. Specimens with a unidirectional layup and with a multidirectional layup were simulated. For a local 3D model, extending to a minimum of about three specimen thicknesses on either side of the delamination front, the results were in good agreement with mixed mode strain energy release rates obtained from computations where the entire specimen had been modeled with solid elements. For large built-up composite structures the shell/3D modeling technique offers a great potential for reducing the model size, since only a relatively small section in the vicinity of the delamination front needs to be modeled with solid elements.

  9. 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.

  10. Sketch on dynamic gesture tracking and analysis exploiting vision-based 3D interface

    NASA Astrophysics Data System (ADS)

    Woo, Woontack; Kim, Namgyu; Wong, Karen; Tadenuma, Makoto

    2000-12-01

    In this paper, we propose a vision-based 3D interface exploiting invisible 3D boxes, arranged in the personal space (i.e. reachable space by the body without traveling), which allows robust yet simple dynamic gesture tracking and analysis, without exploiting complicated sensor-based motion tracking systems. Vision-based gesture tracking and analysis is still a challenging problem, even though we have witnessed rapid advances in computer vision over the last few decades. The proposed framework consists of three main parts, i.e. (1) object segmentation without bluescreen and 3D box initialization with depth information, (2) movement tracking by observing how the body passes through the 3D boxes in the personal space and (3) movement feature extraction based on Laban's Effort theory and movement analysis by mapping features to meaningful symbols using time-delay neural networks. Obviously, exploiting depth information using multiview images improves the performance of gesture analysis by reducing the errors introduced by simple 2D interfaces In addition, the proposed box-based 3D interface lessens the difficulties in both tracking movement in 3D space and in extracting low-level features of the movement. Furthermore, the time-delay neural networks lessens the difficulties in movement analysis by training. Due to its simplicity and robustness, the framework will provide interactive systems, such as ATR I-cubed Tangible Music System or ATR Interactive Dance system, with improved quality of the 3D interface. The proposed simple framework also can be extended to other applications requiring dynamic gesture tracking and analysis on the fly.

  11. 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

  12. 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

  13. Cascaded systems analysis of the 3D NEQ for cone-beam CT and tomosynthesis

    NASA Astrophysics Data System (ADS)

    Tward, D. J.; Siewerdsen, J. H.; Fahrig, R. A.; Pineda, A. R.

    2008-03-01

    Crucial to understanding the factors that govern imaging performance is a rigorous analysis of signal and noise transfer characteristics (e.g., MTF, NPS, and NEQ) applied to a task-based performance metric (e.g., detectability index). This paper advances a theoretical framework for calculation of the NPS, NEQ, and DQE of cone-beam CT (CBCT) and tomosynthesis based on cascaded systems analysis. The model considers the 2D projection NPS propagated through a series of reconstruction stages to yield the 3D NPS, revealing a continuum (from 2D projection radiography to limited-angle tomosynthesis and fully 3D CBCT) for which NEQ and detectability index may be investigated as a function of any system parameter. Factors considered in the cascade include: system geometry; angular extent of source-detector orbit; finite number of views; log-scaling; application of ramp, apodization, and interpolation filters; back-projection; and 3D noise aliasing - all of which have a direct impact on the 3D NEQ and DQE. Calculations of the 3D NPS were found to agree with experimental measurements across a broad range of imaging conditions. The model presents a theoretical framework that unifies 3D Fourier-based performance metrology in tomosynthesis and CBCT, providing a guide to optimization that rigorously considers the system configuration, reconstruction parameters, and imaging task.

  14. 3D Analysis of the Proximal Interphalangeal Joint Kinematics during Flexion

    PubMed Central

    Fürnstahl, Philipp; Gallo, Luigi-Maria; Schweizer, Andreas

    2013-01-01

    Background. Dynamic joint motion recording combined with CT-based 3D bone and joint surface data is accepted as a helpful and precise tool to analyse joint. The purpose of this study is to demonstrate the feasibility of these techniques for quantitative motion analysis of the interphalangeal joint in 3D. Materials and Method. High resolution motion data was combined with an accurate 3D model of a cadaveric index finger. Three light-emitting diodes (LEDs) were used to record dynamic data, and a CT scan of the finger was done for 3D joint surface geometry. The data allowed performing quantitative evaluations such as finite helical axis (FHA) analysis, coordinate system optimization, and measurement of the joint distances in 3D. Results. The FHA varies by 4.9 ± 1.7° on average. On average, the rotation in adduction/abduction and internal/external rotation were 0.3 ± 0.91° and 0.1 ± 0.97°, respectively. During flexion, a translational motion between 0.06 mm and 0.73 mm was observed. Conclusions. The proposed technique and methods appear to be feasible for the accurate assessment and evaluation of the PIP joint motion in 3D. The presented method may help to gain additional insights for the design of prosthetic implants, rehabilitation, and new orthotic devices. PMID:24302972

  15. 3D video analysis of the novel object recognition test in rats.

    PubMed

    Matsumoto, Jumpei; Uehara, Takashi; Urakawa, Susumu; Takamura, Yusaku; Sumiyoshi, Tomiki; Suzuki, Michio; Ono, Taketoshi; Nishijo, Hisao

    2014-10-01

    The novel object recognition (NOR) test has been widely used to test memory function. We developed a 3D computerized video analysis system that estimates nose contact with an object in Long Evans rats to analyze object exploration during NOR tests. The results indicate that the 3D system reproducibly and accurately scores the NOR test. Furthermore, the 3D system captures a 3D trajectory of the nose during object exploration, enabling detailed analyses of spatiotemporal patterns of object exploration. The 3D trajectory analysis revealed a specific pattern of object exploration in the sample phase of the NOR test: normal rats first explored the lower parts of objects and then gradually explored the upper parts. A systematic injection of MK-801 suppressed changes in these exploration patterns. The results, along with those of previous studies, suggest that the changes in the exploration patterns reflect neophobia to a novel object and/or changes from spatial learning to object learning. These results demonstrate that the 3D tracking system is useful not only for detailed scoring of animal behaviors but also for investigation of characteristic spatiotemporal patterns of object exploration. The system has the potential to facilitate future investigation of neural mechanisms underlying object exploration that result from dynamic and complex brain activity. PMID:24991752

  16. Low-cost impact detection and location for automated inspections of 3D metallic based structures.

    PubMed

    Morón, Carlos; Portilla, Marina P; Somolinos, José A; Morales, Rafael

    2015-01-01

    This paper describes a new low-cost means to detect and locate mechanical impacts (collisions) on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing) the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach. PMID:26029951

  17. 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

  18. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  19. Sequence-based identification of 3D structural modules in RNA with RMDetect.

    PubMed

    Cruz, José Almeida; Westhof, Eric

    2011-06-01

    Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data. PMID:21552257

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. 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.

  2. Experimentation of structured light and stereo vision for underwater 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Bruno, F.; Bianco, G.; Muzzupappa, M.; Barone, S.; Razionale, A. V.

    Current research on underwater 3D imaging methods is mainly addressing long range applications like seafloor mapping or surveys of archeological sites and shipwrecks. Recently, there is an increasing need for more accessible and precise close-range 3D acquisition technologies in some application fields like, for example, monitoring the growth of coral reefs or reconstructing underwater archaeological pieces that in most cases cannot be recovered from the seabed. This paper presents the first results of a research project that aims to investigate the possibility of using active optical techniques for the whole-field 3D reconstructions in an underwater environment. In this work we have tested an optical technique, frequently used for in air acquisition, based on the projection of structured lighting patterns acquired by a stereo vision system. We describe the experimental setup used for the underwater tests, which were conducted in a water tank with different turbidity conditions. The tests have evidenced that the quality of 3D reconstruction is acceptable even with high turbidity values, despite the heavy presence of scattering and absorption effects.

  3. CamMedNP: Building the Cameroonian 3D structural natural products database for virtual screening

    PubMed Central

    2013-01-01

    Background Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. Description In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the “drug-likeness” of this database using Lipinski’s “Rule of Five”. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Conclusion CamMedNP could be highly useful for database screening and natural product lead generation programs. PMID:23590173

  4. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

  5. 3D pore-network analysis and permeability estimation of deformation bands hosted in carbonate grainstones.

    NASA Astrophysics Data System (ADS)

    Zambrano, Miller; Tondi, Emanuele; Mancini, Lucia; Trias, F. Xavier; Arzilli, Fabio; Lanzafame, Gabriele; Aibibula, Nijiati

    2016-04-01

    In porous rocks strain is commonly localized in narrow Deformation Bands (DBs), where the petrophysical properties are significantly modified with respect the pristine rock. As a consequence, DBs could have an important effect on production and development of porous reservoirs representing baffles zones or, in some cases, contribute to reservoir compartmentalization. Taking in consideration that the decrease of permeability within DBs is related to changes in the porous network properties (porosity, connectivity) and t