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 on the Puy de Dôme volcano resulting in 12 ERT profiles with approximatively 800 electrodes. We performed two processing stages by inverting independently each profiles in 2D (RES2DINV software) and the complete data set in 3D (EResI). The comparison of the 3D inversion results with those obtained through a conventional 2D inversion process underlined that EResI allows to accurately take into account the random electrodes positioning and reduce out-line artefacts into the inversion models due to positioning errors out of the profile axis. This comparison also highlighted the advantages to integrate several ERT lines to compute the 3D models of complex volcanic structures. Finally, the resulting 3D model allows a better interpretation of the Puy de Dome Volcano.

Three-dimensional magnetotelluric inversion in practice—the electrical conductivity structure of the San Andreas Fault in Central California

NASA Astrophysics Data System (ADS)

Tietze, Kristina; Ritter, Oliver

2013-10-01

3-D inversion techniques have become a widely used tool in magnetotelluric (MT) data interpretation. However, with real data sets, many of the controlling factors for the outcome of 3-D inversion are little explored, such as alignment of the coordinate system, handling and influence of data errors and model regularization. Here we present 3-D inversion results of 169 MT sites from the central San Andreas Fault in California. Previous extensive 2-D inversion and 3-D forward modelling of the data set revealed significant along-strike variation of the electrical conductivity structure. 3-D inversion can recover these features but only if the inversion parameters are tuned in accordance with the particularities of the data set. Based on synthetic 3-D data we explore the model space and test the impacts of a wide range of inversion settings. The tests showed that the recovery of a pronounced regional 2-D structure in inversion of the complete impedance tensor depends on the coordinate system. As interdependencies between data components are not considered in standard 3-D MT inversion codes, 2-D subsurface structures can vanish if data are not aligned with the regional strike direction. A priori models and data weighting, that is, how strongly individual components of the impedance tensor and/or vertical magnetic field transfer functions dominate the solution, are crucial controls for the outcome of 3-D inversion. If deviations from a prior model are heavily penalized, regularization is prone to result in erroneous and misleading 3-D inversion models, particularly in the presence of strong conductivity contrasts. A `good' overall rms misfit is often meaningless or misleading as a huge range of 3-D inversion results exist, all with similarly `acceptable' misfits but producing significantly differing images of the conductivity structures. Reliable and meaningful 3-D inversion models can only be recovered if data misfit is assessed systematically in the frequency-space domain.

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunár, Stanislav; Mackay, Duncan H.

2015-04-20

We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique tomore » consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.« less

Three-dimensional Printed Cardiac Models: Applications in the Field of Medical Education, Cardiovascular Surgery, and Structural Heart Interventions.

PubMed

Valverde, Israel

2017-04-01

In recent years, three-dimensional (3D) printed models have been incorporated into cardiology because of their potential usefulness in enhancing understanding of congenital heart disease, surgical planning, and simulation of structural percutaneous interventions. This review provides an introduction to 3D printing technology and identifies the elements needed to construct a 3D model: the types of imaging modalities that can be used, their minimum quality requirements, and the kinds of 3D printers available. The review also assesses the usefulness of 3D printed models in medical education, specialist physician training, and patient communication. We also review the most recent applications of 3D models in surgical planning and simulation of percutaneous structural heart interventions. Finally, the current limitations of 3D printing and its future directions are discussed to explore potential new applications in this exciting medical field. Copyright © 2016 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

Construction of a three-dimensional interactive model of the skull base and cranial nerves.

PubMed

Kakizawa, Yukinari; Hongo, Kazuhiro; Rhoton, Albert L

2007-05-01

The goal was to develop an interactive three-dimensional (3-D) computerized anatomic model of the skull base for teaching microneurosurgical anatomy and for operative planning. The 3-D model was constructed using commercially available software (Maya 6.0 Unlimited; Alias Systems Corp., Delaware, MD), a personal computer, four cranial specimens, and six dry bones. Photographs from at least two angles of the superior and lateral views were imported to the 3-D software. Many photographs were needed to produce the model in anatomically complex areas. Careful dissection was needed to expose important structures in the two views. Landmarks, including foramen, bone, and dura mater, were used as reference points. The 3-D model of the skull base and related structures was constructed using more than 300,000 remodeled polygons. The model can be viewed from any angle. It can be rotated 360 degrees in any plane using any structure as the focal point of rotation. The model can be reduced or enlarged using the zoom function. Variable transparencies could be assigned to any structures so that the structures at any level can be seen. Anatomic labels can be attached to the structures in the 3-D model for educational purposes. This computer-generated 3-D model can be observed and studied repeatedly without the time limitations and stresses imposed by surgery. This model may offer the potential to create interactive surgical exercises useful in evaluating multiple surgical routes to specific target areas in the skull base.

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

PubMed

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

2016-01-01

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

Canine hippocampal formation composited into three-dimensional structure using MPRAGE.

PubMed

Jung, Mi-Ae; Nahm, Sang-Soep; Lee, Min-Su; Lee, In-Hye; Lee, Ah-Ra; Jang, Dong-Pyo; Kim, Young-Bo; Cho, Zang-Hee; Eom, Ki-Dong

2010-07-01

This study was performed to anatomically illustrate the living canine hippocampal formation in three-dimensions (3D), and to evaluate its relationship to surrounding brain structures. Three normal beagle dogs were scanned on a MR scanner with inversion recovery segmented 3D gradient echo sequence (known as MP-RAGE: Magnetization Prepared Rapid Gradient Echo). The MRI data was manually segmented and reconstructed into a 3D model using the 3D slicer software tool. From the 3D model, the spatial relationships between hippocampal formation and surrounding structures were evaluated. With the increased spatial resolution and contrast of the MPRAGE, the canine hippocampal formation was easily depicted. The reconstructed 3D image allows easy understanding of the hippocampal contour and demonstrates the structural relationship of the hippocampal formation to surrounding structures in vivo.

Three-Dimensional Pathology Specimen Modeling Using "Structure-From-Motion" Photogrammetry: A Powerful New Tool for Surgical Pathology.

PubMed

Turchini, John; Buckland, Michael E; Gill, Anthony J; Battye, Shane

2018-05-30

- Three-dimensional (3D) photogrammetry is a method of image-based modeling in which data points in digital images, taken from offset viewpoints, are analyzed to generate a 3D model. This modeling technique has been widely used in the context of geomorphology and artificial imagery, but has yet to be used within the realm of anatomic pathology. - To describe the application of a 3D photogrammetry system capable of producing high-quality 3D digital models and its uses in routine surgical pathology practice as well as medical education. - We modeled specimens received in the 2 participating laboratories. The capture and photogrammetry process was automated using user control software, a digital single-lens reflex camera, and digital turntable, to generate a 3D model with the output in a PDF file. - The entity demonstrated in each specimen was well demarcated and easily identified. Adjacent normal tissue could also be easily distinguished. Colors were preserved. The concave shapes of any cystic structures or normal convex rounded structures were discernable. Surgically important regions were identifiable. - Macroscopic 3D modeling of specimens can be achieved through Structure-From-Motion photogrammetry technology and can be applied quickly and easily in routine laboratory practice. There are numerous advantages to the use of 3D photogrammetry in pathology, including improved clinicopathologic correlation for the surgeon and enhanced medical education, revolutionizing the digital pathology museum with virtual reality environments and 3D-printing specimen models.

QSAR and 3D QSAR of inhibitors of the epidermal growth factor receptor

NASA Astrophysics Data System (ADS)

Pinto-Bazurco, Mariano; Tsakovska, Ivanka; Pajeva, Ilza

This article reports quantitative structure-activity relationships (QSAR) and 3D QSAR models of 134 structurally diverse inhibitors of the epidermal growth factor receptor (EGFR) tyrosine kinase. Free-Wilson analysis was used to derive the QSAR model. It identified the substituents in aniline, the polycyclic system, and the substituents at the 6- and 7-positions of the polycyclic system as the most important structural features. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used in the 3D QSAR modeling. The steric and electrostatic interactions proved the most important for the inhibitory effect. Both QSAR and 3D QSAR models led to consistent results. On the basis of the statistically significant models, new structures were proposed and their inhibitory activities were predicted.

Automated building of organometallic complexes from 3D fragments.

PubMed

Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

2014-07-28

A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.

A 3D puzzle approach to building protein-DNA structures.

PubMed

Hinton, Deborah M

2017-03-15

Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.

Determination of orthotropic mechanical properties of 3D printed parts for structural health monitoring

NASA Astrophysics Data System (ADS)

Poissenot-Arrigoni, Bastien; Scheyer, Austin; Anton, Steven R.

2017-04-01

The evolution of additive manufacturing has allowed engineers to use 3D printing for many purposes. As a natural consequence of the 3D printing process, the printed object is anisotropic. As part of an ongoing project to embed piezoelectric devices in 3D printed structures for structural health monitoring (SHM), this study aims to find the mechanical properties of the 3D printed material and the influence of different external factors on those properties. The orthotropic mechanical properties of a 3D printed structure are dependent on the printing parameters used to create the structure. In order to develop an orthotropic material model, mechanical properties will be found experimentally from additively manufactured samples created from polylactic acid (PLA) using a consumer-level fused deposition modeling (FDM) printer; the Lulzbot TAZ 6. Nine mechanical constants including three Young's moduli, three Poisson's ratios, and three shear moduli are needed to fully describe the 3D elastic behavior of the material. Printed specimens with different raster orientations and print orientations allow calculation of the different material constants. In this work, seven of the nine mechanical constants were found. Two shear moduli were unable to be measured due to difficulties in printing two of the sample orientations. These mechanical properties are needed in order to develop orthotropic material models of systems employing 3D printed PLA. The results from this paper will be used to create a model of a piezoelectric transducer embedded in a 3D printed structure for structural health monitoring.

Accurate facade feature extraction method for buildings from three-dimensional point cloud data considering structural information

NASA Astrophysics Data System (ADS)

Wang, Yongzhi; Ma, Yuqing; Zhu, A.-xing; Zhao, Hui; Liao, Lixia

2018-05-01

Facade features represent segmentations of building surfaces and can serve as a building framework. Extracting facade features from three-dimensional (3D) point cloud data (3D PCD) is an efficient method for 3D building modeling. By combining the advantages of 3D PCD and two-dimensional optical images, this study describes the creation of a highly accurate building facade feature extraction method from 3D PCD with a focus on structural information. The new extraction method involves three major steps: image feature extraction, exploration of the mapping method between the image features and 3D PCD, and optimization of the initial 3D PCD facade features considering structural information. Results show that the new method can extract the 3D PCD facade features of buildings more accurately and continuously. The new method is validated using a case study. In addition, the effectiveness of the new method is demonstrated by comparing it with the range image-extraction method and the optical image-extraction method in the absence of structural information. The 3D PCD facade features extracted by the new method can be applied in many fields, such as 3D building modeling and building information modeling.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Transverse Tensile Properties of 3 Dimension-4 Directional Braided Cf/SiC Composite Based on Double-Scale Model

NASA Astrophysics Data System (ADS)

Niu, Xuming; Sun, Zhigang; Song, Yingdong

2017-11-01

In this thesis, a double-scale model for 3 Dimension-4 directional(3D-4d) braided C/SiC composites(CMCs) has been proposed to investigate mechanical properties of it. The double-scale model involves micro-scale which takes fiber/matrix/porosity in fibers tows into consideration and the unit cell scale which considers the 3D-4d braiding structure. Basing on the Micro-optical photographs of composite, we can build a parameterized finite element model that reflects structure of 3D-4d braided composites. The mechanical properties of fiber tows in transverse direction are studied by combining the crack band theory for matrix cracking and cohesive zone model for interface debonding. Transverse tensile process of 3D-4d CMCs can be simulated by introducing mechanical properties of fiber tows into finite element of 3D-4d braided CMCs. Quasi-static tensile tests of 3D-4d braided CMCs have been performed with PWS-100 test system. The predicted tensile stress-strain curve by the double scale model finds good agreement with the experimental results.

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

NASA Astrophysics Data System (ADS)

Zhu, Luoding

2017-11-01

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

Utilisation of three-dimensional printed heart models for operative planning of complex congenital heart defects.

PubMed

Olejník, Peter; Nosal, Matej; Havran, Tomas; Furdova, Adriana; Cizmar, Maros; Slabej, Michal; Thurzo, Andrej; Vitovic, Pavol; Klvac, Martin; Acel, Tibor; Masura, Jozef

2017-01-01

To evaluate the accuracy of the three-dimensional (3D) printing of cardiovascular structures. To explore whether utilisation of 3D printed heart replicas can improve surgical and catheter interventional planning in patients with complex congenital heart defects. Between December 2014 and November 2015 we fabricated eight cardiovascular models based on computed tomography data in patients with complex spatial anatomical relationships of cardiovascular structures. A Bland-Altman analysis was used to assess the accuracy of 3D printing by comparing dimension measurements at analogous anatomical locations between the printed models and digital imagery data, as well as between printed models and in vivo surgical findings. The contribution of 3D printed heart models for perioperative planning improvement was evaluated in the four most representative patients. Bland-Altman analysis confirmed the high accuracy of 3D cardiovascular printing. Each printed model offered an improved spatial anatomical orientation of cardiovascular structures. Current 3D printers can produce authentic copies of patients` cardiovascular systems from computed tomography data. The use of 3D printed models can facilitate surgical or catheter interventional procedures in patients with complex congenital heart defects due to better preoperative planning and intraoperative orientation.

Gis-Based Smart Cartography Using 3d Modeling

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization.

PubMed

Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Pietal, Michal J; Luo, Oscar J; Sadowski, Michał; Li, Xingwang; Radew, Kamen; Ruan, Yijun; Plewczynski, Dariusz

2016-12-01

ChIA-PET is a high-throughput mapping technology that reveals long-range chromatin interactions and provides insights into the basic principles of spatial genome organization and gene regulation mediated by specific protein factors. Recently, we showed that a single ChIA-PET experiment provides information at all genomic scales of interest, from the high-resolution locations of binding sites and enriched chromatin interactions mediated by specific protein factors, to the low resolution of nonenriched interactions that reflect topological neighborhoods of higher-order chromosome folding. This multilevel nature of ChIA-PET data offers an opportunity to use multiscale 3D models to study structural-functional relationships at multiple length scales, but doing so requires a structural modeling platform. Here, we report the development of 3D-GNOME (3-Dimensional Genome Modeling Engine), a complete computational pipeline for 3D simulation using ChIA-PET data. 3D-GNOME consists of three integrated components: a graph-distance-based heat map normalization tool, a 3D modeling platform, and an interactive 3D visualization tool. Using ChIA-PET and Hi-C data derived from human B-lymphocytes, we demonstrate the effectiveness of 3D-GNOME in building 3D genome models at multiple levels, including the entire genome, individual chromosomes, and specific segments at megabase (Mb) and kilobase (kb) resolutions of single average and ensemble structures. Further incorporation of CTCF-motif orientation and high-resolution looping patterns in 3D simulation provided additional reliability of potential biologically plausible topological structures. © 2016 Szałaj et al.; Published by Cold Spring Harbor Laboratory Press.

Modeling ECM fiber formation: structure information extracted by analysis of 2D and 3D image sets

NASA Astrophysics Data System (ADS)

Wu, Jun; Voytik-Harbin, Sherry L.; Filmer, David L.; Hoffman, Christoph M.; Yuan, Bo; Chiang, Ching-Shoei; Sturgis, Jennis; Robinson, Joseph P.

2002-05-01

Recent evidence supports the notion that biological functions of extracellular matrix (ECM) are highly correlated to its structure. Understanding this fibrous structure is very crucial in tissue engineering to develop the next generation of biomaterials for restoration of tissues and organs. In this paper, we integrate confocal microscopy imaging and image-processing techniques to analyze the structural properties of ECM. We describe a 2D fiber middle-line tracing algorithm and apply it via Euclidean distance maps (EDM) to extract accurate fibrous structure information, such as fiber diameter, length, orientation, and density, from single slices. Based on a 2D tracing algorithm, we extend our analysis to 3D tracing via Euclidean distance maps to extract 3D fibrous structure information. We use computer simulation to construct the 3D fibrous structure which is subsequently used to test our tracing algorithms. After further image processing, these models are then applied to a variety of ECM constructions from which results of 2D and 3D traces are statistically analyzed.

Research and development of a digital design system for hull structures

NASA Astrophysics Data System (ADS)

Zhan, Yi-Ting; Ji, Zhuo-Shang; Liu, Yin-Dong

2007-06-01

Methods used for digital ship design were studied and formed the basis of a proposed frame model suitable for ship construction modeling. Based on 3-D modeling software, a digital design system for hull structures was developed. Basic software systems for modeling, modifying, and assembly simulation were developed. The system has good compatibility, and models created by it can be saved in different 3-D file formats, and 2D engineering drawings can be output directly. The model can be modified dynamically, overcoming the necessity of repeated modifications during hull structural design. Through operations such as model construction, intervention inspection, and collision detection, problems can be identified and modified during the hull structural design stage. Technologies for centralized control of the system, database management, and 3-D digital design are integrated into this digital model in the preliminary design stage of shipbuilding.

Fast Geometric Consensus Approach for Protein Model Quality Assessment

PubMed Central

Adamczak, Rafal; Pillardy, Jaroslaw; Vallat, Brinda K.

2011-01-01

Abstract Model quality assessment (MQA) is an integral part of protein structure prediction methods that typically generate multiple candidate models. The challenge lies in ranking and selecting the best models using a variety of physical, knowledge-based, and geometric consensus (GC)-based scoring functions. In particular, 3D-Jury and related GC methods assume that well-predicted (sub-)structures are more likely to occur frequently in a population of candidate models, compared to incorrectly folded fragments. While this approach is very successful in the context of diversified sets of models, identifying similar substructures is computationally expensive since all pairs of models need to be superimposed using MaxSub or related heuristics for structure-to-structure alignment. Here, we consider a fast alternative, in which structural similarity is assessed using 1D profiles, e.g., consisting of relative solvent accessibilities and secondary structures of equivalent amino acid residues in the respective models. We show that the new approach, dubbed 1D-Jury, allows to implicitly compare and rank N models in O(N) time, as opposed to quadratic complexity of 3D-Jury and related clustering-based methods. In addition, 1D-Jury avoids computationally expensive 3D superposition of pairs of models. At the same time, structural similarity scores based on 1D profiles are shown to correlate strongly with those obtained using MaxSub. In terms of the ability to select the best models as top candidates 1D-Jury performs on par with other GC methods. Other potential applications of the new approach, including fast clustering of large numbers of intermediate structures generated by folding simulations, are discussed as well. PMID:21244273

Validation of clay modeling as a learning tool for the periventricular structures of the human brain.

PubMed

Akle, Veronica; Peña-Silva, Ricardo A; Valencia, Diego M; Rincón-Perez, Carlos W

2018-03-01

Visualizing anatomical structures and functional processes in three dimensions (3D) are important skills for medical students. However, contemplating 3D structures mentally and interpreting biomedical images can be challenging. This study examines the impact of a new pedagogical approach to teaching neuroanatomy, specifically how building a 3D-model from oil-based modeling clay affects learners' understanding of periventricular structures of the brain among undergraduate medical students in Colombia. Students were provided with an instructional video before building the models of the structures, and thereafter took a computer-based quiz. They then brought their clay models to class where they answered questions about the structures via interactive response cards. Their knowledge of periventricular structures was assessed with a paper-based quiz. Afterward, a focus group was conducted and a survey was distributed to understand students' perceptions of the activity, as well as the impact of the intervention on their understanding of anatomical structures in 3D. Quiz scores of students that constructed the models were significantly higher than those taught the material in a more traditional manner (P < 0.05). Moreover, the modeling activity reduced time spent studying the topic and increased understanding of spatial relationships between structures in the brain. The results demonstrated a significant difference between genders in their self-perception of their ability to contemplate and rotate structures mentally (P < 0.05). The study demonstrated that the construction of 3D clay models in combination with autonomous learning activities was a valuable and efficient learning tool in the anatomy course, and that additional models could be designed to promote deeper learning of other neuroanatomy topics. Anat Sci Educ 11: 137-145. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

Comparative Protein Structure Modeling Using MODELLER.

PubMed

Webb, Benjamin; Sali, Andrej

2014-09-08

Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. Copyright © 2014 John Wiley & Sons, Inc.

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

Cities and urban areas entities such as building structures are becoming more complex as the modern human civilizations continue to evolve. The ability to plan and manage every territory especially the urban areas is very important to every government in the world. Planning and managing cities and urban areas based on printed maps and 2D data are getting insufficient and inefficient to cope with the complexity of the new developments in big cities. The emergence of 3D city models have boosted the efficiency in analysing and managing urban areas as the 3D data are proven to represent the real world object more accurately. It has since been adopted as the new trend in buildings and urban management and planning applications. Nowadays, many countries around the world have been generating virtual 3D representation of their major cities. The growing interest in improving the usability of 3D city models has resulted in the development of various tools for analysis based on the 3D city models. Today, 3D city models are generated for various purposes such as for tourism, location-based services, disaster management and urban planning. Meanwhile, modelling 3D objects are getting easier with the emergence of the user-friendly tools for 3D modelling available in the market. Generating 3D buildings with high accuracy also has become easier with the availability of airborne Lidar and terrestrial laser scanning equipments. The availability and accessibility to this technology makes it more sensible to analyse buildings in urban areas using 3D data as it accurately represent the real world objects. The Open Geospatial Consortium (OGC) has accepted CityGML specifications as one of the international standards for representing and exchanging spatial data, making it easier to visualize, store and manage 3D city models data efficiently. CityGML able to represents the semantics, geometry, topology and appearance of 3D city models in five well-defined Level-of-Details (LoD), namely LoD0 to LoD4. The accuracy and structural complexity of the 3D objects increases with the LoD level where LoD0 is the simplest LoD (2.5D; Digital Terrain Model (DTM) + building or roof print) while LoD4 is the most complex LoD (architectural details with interior structures). Semantic information is one of the main components in CityGML and 3D City Models, and provides important information for any analyses. However, more often than not, the semantic information is not available for the 3D city model due to the unstandardized modelling process. One of the examples is where a building is normally generated as one object (without specific feature layers such as Roof, Ground floor, Level 1, Level 2, Block A, Block B, etc). This research attempts to develop a method to improve the semantic data updating process by segmenting the 3D building into simpler parts which will make it easier for the users to select and update the semantic information. The methodology is implemented for 3D buildings in LoD2 where the buildings are generated without architectural details but with distinct roof structures. This paper also introduces hybrid semantic-geometric 3D segmentation method that deals with hierarchical segmentation of a 3D building based on its semantic value and surface characteristics, fitted by one of the predefined primitives. For future work, the segmentation method will be implemented as part of the change detection module that can detect any changes on the 3D buildings, store and retrieve semantic information of the changed structure, automatically updates the 3D models and visualize the results in a userfriendly graphical user interface (GUI).

Quality Assessment and Comparison of Smartphone and Leica C10 Laser Scanner Based Point Clouds

NASA Astrophysics Data System (ADS)

Sirmacek, Beril; Lindenbergh, Roderik; Wang, Jinhu

2016-06-01

3D urban models are valuable for urban map generation, environment monitoring, safety planning and educational purposes. For 3D measurement of urban structures, generally airborne laser scanning sensors or multi-view satellite images are used as a data source. However, close-range sensors (such as terrestrial laser scanners) and low cost cameras (which can generate point clouds based on photogrammetry) can provide denser sampling of 3D surface geometry. Unfortunately, terrestrial laser scanning sensors are expensive and trained persons are needed to use them for point cloud acquisition. A potential effective 3D modelling can be generated based on a low cost smartphone sensor. Herein, we show examples of using smartphone camera images to generate 3D models of urban structures. We compare a smartphone based 3D model of an example structure with a terrestrial laser scanning point cloud of the structure. This comparison gives us opportunity to discuss the differences in terms of geometrical correctness, as well as the advantages, disadvantages and limitations in data acquisition and processing. We also discuss how smartphone based point clouds can help to solve further problems with 3D urban model generation in a practical way. We show that terrestrial laser scanning point clouds which do not have color information can be colored using smartphones. The experiments, discussions and scientific findings might be insightful for the future studies in fast, easy and low-cost 3D urban model generation field.

The influence of computational strategy on prediction of mechanical stress in carotid atherosclerotic plaques: comparison of 2D structure-only, 3D structure-only, one-way and fully coupled fluid-structure interaction analyses.

PubMed

Huang, Yuan; Teng, Zhongzhao; Sadat, Umar; Graves, Martin J; Bennett, Martin R; Gillard, Jonathan H

2014-04-11

Compositional and morphological features of carotid atherosclerotic plaques provide complementary information to luminal stenosis in predicting clinical presentations. However, they alone cannot predict cerebrovascular risk. Mechanical stress within the plaque induced by cyclical changes in blood pressure has potential to assess plaque vulnerability. Various modeling strategies have been employed to predict stress, including 2D and 3D structure-only, 3D one-way and fully coupled fluid-structure interaction (FSI) simulations. However, differences in stress predictions using different strategies have not been assessed. Maximum principal stress (Stress-P1) within 8 human carotid atherosclerotic plaques was calculated based on geometry reconstructed from in vivo computerized tomography and high resolution, multi-sequence magnetic resonance images. Stress-P1 within the diseased region predicted by 2D and 3D structure-only, and 3D one-way FSI simulations were compared to 3D fully coupled FSI analysis. Compared to 3D fully coupled FSI, 2D structure-only simulation significantly overestimated stress level (94.1 kPa [65.2, 117.3] vs. 85.5 kPa [64.4, 113.6]; median [inter-quartile range], p=0.0004). However, when slices around the bifurcation region were excluded, stresses predicted by 2D structure-only simulations showed a good correlation (R(2)=0.69) with values obtained from 3D fully coupled FSI analysis. 3D structure-only model produced a small yet statistically significant stress overestimation compared to 3D fully coupled FSI (86.8 kPa [66.3, 115.8] vs. 85.5 kPa [64.4, 113.6]; p<0.0001). In contrast, one-way FSI underestimated stress compared to 3D fully coupled FSI (78.8 kPa [61.1, 100.4] vs. 85.5 kPa [64.4, 113.7]; p<0.0001). A 3D structure-only model seems to be a computationally inexpensive yet reasonably accurate approximation for stress within carotid atherosclerotic plaques with mild to moderate luminal stenosis as compared to fully coupled FSI analysis. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

PubMed

Hayat, Sikander; Sander, Chris; Marks, Debora S; Elofsson, Arne

2015-04-28

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.

Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs

PubMed Central

Delparte, D; Gates, RD; Takabayashi, M

2015-01-01

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems. PMID:26207190

Three-Dimensional Sensitivity Kernels of Z/H Amplitude Ratios of Surface and Body Waves

NASA Astrophysics Data System (ADS)

Bao, X.; Shen, Y.

2017-12-01

The ellipticity of Rayleigh wave particle motion, or Z/H amplitude ratio, has received increasing attention in inversion for shallow Earth structures. Previous studies of the Z/H ratio assumed one-dimensional (1D) velocity structures beneath the receiver, ignoring the effects of three-dimensional (3D) heterogeneities on wave amplitudes. This simplification may introduce bias in the resulting models. Here we present 3D sensitivity kernels of the Z/H ratio to Vs, Vp, and density perturbations, based on finite-difference modeling of wave propagation in 3D structures and the scattering-integral method. Our full-wave approach overcomes two main issues in previous studies of Rayleigh wave ellipticity: (1) the finite-frequency effects of wave propagation in 3D Earth structures, and (2) isolation of the fundamental mode Rayleigh waves from Rayleigh wave overtones and converted Love waves. In contrast to the 1D depth sensitivity kernels in previous studies, our 3D sensitivity kernels exhibit patterns that vary with azimuths and distances to the receiver. The laterally-summed 3D sensitivity kernels and 1D depth sensitivity kernels, based on the same homogeneous reference model, are nearly identical with small differences that are attributable to the single period of the 1D kernels and a finite period range of the 3D kernels. We further verify the 3D sensitivity kernels by comparing the predictions from the kernels with the measurements from numerical simulations of wave propagation for models with various small-scale perturbations. We also calculate and verify the amplitude kernels for P waves. This study shows that both Rayleigh and body wave Z/H ratios provide vertical and lateral constraints on the structure near the receiver. With seismic arrays, the 3D kernels afford a powerful tool to use the Z/H ratios to obtain accurate and high-resolution Earth models.

Creating Physical 3D Stereolithograph Models of Brain and Skull

PubMed Central

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

2007-01-01

The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine. PMID:17971879

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

PubMed

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

2010-07-01

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs.dtu.dk/services/CPHmodels/.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Generalization Technique for 2D+SCALE Dhe Data Model

NASA Astrophysics Data System (ADS)

Karim, Hairi; Rahman, Alias Abdul; Boguslawski, Pawel

2016-10-01

Different users or applications need different scale model especially in computer application such as game visualization and GIS modelling. Some issues has been raised on fulfilling GIS requirement of retaining the details while minimizing the redundancy of the scale datasets. Previous researchers suggested and attempted to add another dimension such as scale or/and time into a 3D model, but the implementation of scale dimension faces some problems due to the limitations and availability of data structures and data models. Nowadays, various data structures and data models have been proposed to support variety of applications and dimensionality but lack research works has been conducted in terms of supporting scale dimension. Generally, the Dual Half Edge (DHE) data structure was designed to work with any perfect 3D spatial object such as buildings. In this paper, we attempt to expand the capability of the DHE data structure toward integration with scale dimension. The description of the concept and implementation of generating 3D-scale (2D spatial + scale dimension) for the DHE data structure forms the major discussion of this paper. We strongly believed some advantages such as local modification and topological element (navigation, query and semantic information) in scale dimension could be used for the future 3D-scale applications.

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.

Homology modeling a fast tool for drug discovery: current perspectives.

PubMed

Vyas, V K; Ukawala, R D; Ghate, M; Chintha, C

2012-01-01

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.

Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives

PubMed Central

Vyas, V. K.; Ukawala, R. D.; Ghate, M.; Chintha, C.

2012-01-01

Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery. PMID:23204616

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

PubMed

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-10-01

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

PF2 fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps

PubMed Central

Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje; Bajaj, Chandrajit

2015-01-01

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF2 fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF2 fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF2 fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF2 fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF2 fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF2 fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search. PMID:26469938

Combined aerial and terrestrial images for complete 3D documentation of Singosari Temple based on Structure from Motion algorithm

NASA Astrophysics Data System (ADS)

Hidayat, Husnul; Cahyono, A. B.

2016-11-01

Singosaritemple is one of cultural heritage building in East Java, Indonesia which was built in 1300s and restorated in 1934-1937. Because of its history and importance, complete documentation of this temple is required. Nowadays with the advent of low cost UAVs combining aerial photography with terrestrial photogrammetry gives more complete data for 3D documentation. This research aims to make complete 3D model of this landmark from aerial and terrestrial photographs with Structure from Motion algorithm. To establish correct scale, position, and orientation, the final 3D model was georeferenced with Ground Control Points in UTM 49S coordinate system. The result shows that all facades, floor, and upper structures can be modeled completely in 3D. In terms of 3D coordinate accuracy, the Root Mean Square Errors (RMSEs) are RMSEx=0,041 m; RMSEy=0,031 m; RMSEz=0,049 m which represent 0.071 m displacement in 3D space. In addition the mean difference of lenght measurements of the object is 0,057 m. With this accuracy, this method can be used to map the site up to 1:237 scale. Although the accuracy level is still in centimeters, the combined aerial and terrestrial photographs with Structure from Motion algorithm can provide complete and visually interesting 3D model.

2D-3D MIGRATION AND CONFORMATIONAL MULTIPLICATION OF CHEMICALS IN LARGE CHEMICAL INVENTORIES

EPA Science Inventory

Chemical interactions are three-dimensional (3D) in nature and require modeling chemicals as 3D entities. In turn, using 3D models of chemicals leads to the realization that a single 2D structure can have hundreds of different conformations, and the electronic properties of these...

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

PubMed

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

2016-07-08

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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

CAD-Based Modeling of Advanced Rotary Wing Structures for Integrated 3-D Aeromechanics Analysis

NASA Astrophysics Data System (ADS)

Staruk, William

This dissertation describes the first comprehensive use of integrated 3-D aeromechanics modeling, defined as the coupling of 3-D solid finite element method (FEM) structural dynamics with 3-D computational fluid dynamics (CFD), for the analysis of a real helicopter rotor. The development of this new methodology (a departure from how rotor aeroelastic analysis has been performed for 40 years), its execution on a real rotor, and the fundamental understanding of aeromechanics gained from it, are the key contributions of this dissertation. This work also presents the first CFD/CSD analysis of a tiltrotor in edgewise flight, revealing many of its unique loading mechanisms. The use of 3-D FEM, integrated with a trim solver and aerodynamics modeling, has the potential to enhance the design of advanced rotors by overcoming fundamental limitations of current generation beam-based analysis tools and offering integrated internal dynamic stress and strain predictions for design. Two primary goals drove this research effort: 1) developing a methodology to create 3-D CAD-based brick finite element models of rotors including multibody joints, controls, and aerodynamic interfaces, and 2) refining X3D, the US Army's next generation rotor structural dynamics solver featuring 3-D FEM within a multibody formulation with integrated aerodynamics, to model a tiltrotor in the edgewise conversion flight regime, which drives critical proprotor structural loads. Prior tiltrotor analysis has primarily focused on hover aerodynamics with rigid blades or forward flight whirl-flutter stability with simplified aerodynamics. The first goal was met with the development of a detailed methodology for generating multibody 3-D structural models, starting from CAD geometry, continuing to higher-order hexahedral finite element meshing, to final assembly of the multibody model by creating joints, assigning material properties, and defining the aerodynamic interface. Several levels of verification and validation were carried out systematically, covering formulation, model accuracy, and accuracy of the physics of the problem and the many complex coupled aeromechanical phenomena that characterize the behavior of a tiltrotor in the conversion corridor. Compatibility of the new structural analysis models with X3D is demonstrated using analytical test cases, including 90° twisted beams and thick composite plates, and a notional bearingless rotor. Prediction of deformations and stresses in composite beams and plates is validated and verified against experimental measurements, theory, and state-of-the-art beam models. The second goal was met through integrated analysis of the Tilt Rotor Aeroacoustic Model (TRAM) proprotor using X3D coupled to Helios--the US Army's next generation CFD framework featuring a high fidelity Reynolds-average Navier-Stokes (RANS) structured/unstructured overset solver--as well as low order aerodynamic models. Although development of CFD was not part of this work, coupling X3D with Helios was, including establishing consistent interface definitions for blade deformations (for CFD mesh motion), aerodynamic interfaces (for loads transfer), and rotor control angles (for trim). It is expected that this method and solver will henceforth be an integral part of the Helios framework, providing an equal fidelity of representation for fluids and structures in the development of future advanced rotor systems. Structural dynamics analysis of the TRAM model show accurate prediction of the lower natural frequencies, demonstrating the ability to model advanced rotors from first principles using 3-D structural dynamics, and a study of how joint properties affect these frequencies reveals how X3D can be used as a detailed design tool. The CFD/CSD analysis reveals accurate prediction of rotor performance and airloads in edgewise flight when compared to wind tunnel test data. Structural blade loads trends are well predicted at low thrust, but a 3/rev component of flap and lag bending moment appearing in test data at high thrust remains a mystery. Efficiently simulating a gimbaled rotor is not trivial; a time-domain method with only a single blade model is proposed and tested. The internal stress in the blade, particularly at its root where the gimbal action has major influence, is carefully examined, revealing complex localized loading patterns.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Soft tissue models: easy and inexpensive flexible 3D printing as a help in surgical planning of cardiovascular disorders

NASA Astrophysics Data System (ADS)

Starosolski, Zbigniew; Ezon, David S.; Krishnamurthy, Rajesh; Dodd, Nicholas; Heinle, Jeffrey; Mckenzie, Dean E.; Annapragada, Ananth

2017-03-01

We developed a technology that allows a simple desktop 3D printer with dual extruder to fabricate 3D flexible models of Major AortoPulmonary Collateral Arteries. The study was designed to assess whether the flexible 3D printed models could help during surgical planning phase. Simple FDM 3D printers are inexpensive, versatile in use and easy to maintain, but complications arise when the designed model is complex and has tubular structures with small diameter less than 2mm. The advantages of FDM printers are cost and simplicity of use. We use precisely selected materials to overcome the obstacles listed above. Dual extruder allows to use two different materials while printing, which is especially important in the case of fragile structures like pulmonary vessels and its supporting structures. The latter should not be removed by hand to avoid a truncation of the model. We utilize the water soluble PVA as a supporting structure and Poro-Lay filament for flexible model of AortoPulmonary collateral arteries. Poro-Lay filament is different as compared to all the other flexible ones like polymer-based. Poro-Lay is rigid while printing and this allows printing of structures small in diameter. It achieves flexibility after washing out of printed model with water. It becomes soft in touch and gelatinous. Using both PVA and Poro-Lay gives a huge advantage allowing to wash out the supporting structures and achieve flexibility in one washing operation, saving time and avoiding human error with cleaning the model. We evaluated 6 models for MAPCAS surgical planning study. This approach is also cost-effective - an average cost of materials for print is less than $15; models are printed in facility without any delays. Flexibility of 3D printed models approximate soft tissues properly, mimicking Aortopulmonary collateral arteries. Second utilization models has educational value for both residents and patients' family. Simplification of 3D flexible process could help in other models of soft tissue pathologies like aneurysms, ventricular septal defects and other vascular anomalies.

Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

NASA Astrophysics Data System (ADS)

Maesano, Francesco E.; D'Ambrogi, Chiara

2017-02-01

We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

Single High Fidelity Geometric Data Sets for LCM - Model Requirements

DTIC Science & Technology

2006-11-01

are extensive single 3D CAD data models incorporating hull structure, propulsion, steering, piping , electrical, HVAC and other systems, which make...single 3D CAD data models incorporating hull structure, propulsion, steering, piping , electrical, HVAC and other systems. During this same period...be sufficiently flexible to accommodate the diverse requirements of various types of structural analyses. Section Properties & Material Data

Three-dimensional sinus imaging as an adjunct to two-dimensional imaging to accelerate education and improve spatial orientation.

PubMed

Yao, William C; Regone, Rachel M; Huyhn, Nancy; Butler, E Brian; Takashima, Masayoshi

2014-03-01

Develop a novel three-dimensional (3-D) anatomical model to assist in improving spatial knowledge of the skull base, paranasal sinuses, and adjacent structures, and validate the utilization of 3-D reconstruction to augment two-dimensional (2-D) computed tomography (CT) for the training of medical students and otolaryngology-head and neck surgery residents. Prospective study. A study of 18 subjects studying sinus anatomy was conducted at a tertiary academic center during the 2011 to 2012 academic year. An image processing and 3-D modeling program was used to create a color coded 3-D scalable/layerable/rotatable model of key paranasal and skull base structures from a 2-D high-resolution sinus CT scan. Subjects received instruction of the sinus anatomy in two sessions, first through review of a 2-D CT sinus scan, followed by an educational module of the 3-D reconstruction. After each session, subjects rated their knowledge of the sinus and adjacent structures on a self-assessment questionnaire. Significant improvement in the perceived understanding of the anatomy was noted after the 3-D educational module session when compared to the 2-D CT session alone (P < .01). Every subject believed the addition of 3-D imaging accelerated their education of sinus anatomy and recommended its use to others. The impression of the learners was that a 3-D educational module, highlighting key structures, is a highly effective tool to enhance the education of medical students and otolaryngology residents in sinus and skull base anatomy and its adjacent structures, specifically in conceptualizing the spatial orientation of these structures. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

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/.

Structural and congenital heart disease interventions: the role of three-dimensional printing.

PubMed

Meier, L M; Meineri, M; Qua Hiansen, J; Horlick, E M

2017-02-01

Advances in catheter-based interventions in structural and congenital heart disease have mandated an increased demand for three-dimensional (3D) visualisation of complex cardiac anatomy. Despite progress in 3D imaging modalities, the pre- and periprocedural visualisation of spatial anatomy is relegated to two-dimensional flat screen representations. 3D printing is an evolving technology based on the concept of additive manufacturing, where computerised digital surface renders are converted into physical models. Printed models replicate complex structures in tangible forms that cardiovascular physicians and surgeons can use for education, preprocedural planning and device testing. In this review we discuss the different steps of the 3D printing process, which include image acquisition, segmentation, printing methods and materials. We also examine the expanded applications of 3D printing in the catheter-based treatment of adult patients with structural and congenital heart disease while highlighting the current limitations of this technology in terms of segmentation, model accuracy and dynamic capabilities. Furthermore, we provide information on the resources needed to establish a hospital-based 3D printing laboratory.

Development of Three-Dimensional Dental Scanning Apparatus Using Structured Illumination

PubMed Central

Park, Anjin; Lee, Byeong Ha; Eom, Joo Beom

2017-01-01

We demonstrated a three-dimensional (3D) dental scanning apparatus based on structured illumination. A liquid lens was used for tuning focus and a piezomotor stage was used for the shift of structured light. A simple algorithm, which detects intensity modulation, was used to perform optical sectioning with structured illumination. We reconstructed a 3D point cloud, which represents the 3D coordinates of the digitized surface of a dental gypsum cast by piling up sectioned images. We performed 3D registration of an individual 3D point cloud, which includes alignment and merging the 3D point clouds to exhibit a 3D model of the dental cast. PMID:28714897

APPLICATION OF THE 3D MODEL OF RAILWAY VIADUCTS TO COST ESTIMATION AND CONSTRUCTION

NASA Astrophysics Data System (ADS)

Fujisawa, Yasuo; Yabuki, Nobuyoshi; Igarashi, Zenichi; Yoshino, Hiroyuki

Three dimensional models of civil engineering structures are only partially used in either design or construction but not both. Research on integration of design, cost estimation and construction by 3Dmodels has not been heard in civil engineering domain yet. Using continuously a 3D product model of a structure from design to construction through estimation should improve the efficiency and decrease the occurrence of mistakes, hence enhancing the quality. In this research, we investigated the current practices of flow from design to construction, particularly focusing on cost estimation. Then, we identified advantages and issues on utilization of 3D design models to estimation and construction by applying 3D models to an actual railway construction project.

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

PubMed

Nebel, Jean-Christophe

2006-05-15

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

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

PubMed

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

The objective of this study was to assess the clinical feasibility of generating 3D printing models of left atrial appendage (LAA) using real-time 3D transesophageal echocardiogram (TEE) data for preoperative reference of LAA occlusion. Percutaneous LAA occlusion can effectively prevent patients with atrial fibrillation from stroke. However, the anatomical structure of LAA is so complicated that adequate information of its structure is essential for successful LAA occlusion. Emerging 3D printing technology has the demonstrated potential to structure more accurately than conventional imaging modalities by creating tangible patient-specific models. Typically, 3D printing data sets are acquired from CT and MRI, which may involve intravenous contrast, sedation, and ionizing radiation. It has been reported that 3D models of LAA were successfully created by the data acquired from CT. However, 3D printing of the LAA using real-time 3D TEE data has not yet been explored. Acquisition of 3D transesophageal echocardiographic data from 8 patients with atrial fibrillation was performed using the Philips EPIQ7 ultrasound system. Raw echocardiographic image data were opened in Philips QLAB and converted to 'Cartesian DICOM' format and imported into Mimics® software to create 3D models of LAA, which were printed using a rubber-like material. The printed 3D models were then used for preoperative reference and procedural simulation in LAA occlusion. We successfully printed LAAs of 8 patients. Each LAA costs approximately CNY 800-1,000 and the total process takes 16-17 h. Seven of the 8 Watchman devices predicted by preprocedural 2D TEE images were of the same sizes as those placed in the real operation. Interestingly, 3D printing models were highly reflective of the shape and size of LAAs, and all device sizes predicted by the 3D printing model were fully consistent with those placed in the real operation. Also, the 3D printed model could predict operating difficulty and the presence of a peridevice leak. 3D printing of the LAA using real-time 3D transesophageal echocardiographic data has a perfect and rapid application in LAA occlusion to assist with physician planning and decision making. © 2016 S. Karger AG, Basel.

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

PubMed

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

2018-05-12

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

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

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

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 3Å. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

Teaching and Learning Structural Geology Using SketchUp

NASA Astrophysics Data System (ADS)

Rey, Patrice

2017-04-01

The books and maps we read, the posters we pin on our walls, the TV sets and computer monitors we spend hours watching, the white (or black) boards we use to teach, all reduce our world into planar images. As a result, and through years of oblivious practice, our brain is conditioned to understand the world in two dimensions (2D) only. As structural geologists, we know that the most challenging aspect of teaching and learning structural geology is that we need to be able to mentally manipulate 2D and three-dimensional (3D) objects. Although anyone can learn through practice the art of spatial visualisation, the fact remains that the initial stages of learning structural geology are for many students very challenging, as we naively use 2D images to teach 3D concepts. While interactive 3D holography is not far away, some inexpensive tools already exist allowing us to generate interactive computer images, the free rotation, scaling and manipulation of which can help students to quickly grasp the geometry and internal architecture of 3D objects. Recently, I have experimented with SketchUp (works on Mac and Windows). SketchUp was initially released in 2000 by @Last Software, as a 3D modelling tool for architects, designers and filmmakers. It was acquired by Google in 2006 to further the development of GoogleEarth. Google released SketchUp for free, and provided a portal named 3D Warehouse for users to share their models. Google sold SketchUp to Trimble Navigation in 2012, which added Extension Warehouse for users to distribute add-ons. SketchUp models can be exported in a number of formats including .dae (digital asset exchange) useful to embed interactive 3D models into iBooks and html5 documents, and .kmz (keyhole markup language zipped) to embed interactive 3D models and cross-sections into GoogleEarth. SketchUp models can be exported into 3D pdf through the add-on SimLab, and .stl for 3D printing through the add-on SketchUp STL. A free licence is available for students and educators (SketchUp Make), and a few hundred Euros will give you access to SketchUp Pro. Having the capacity to use 3D interactive sketches instead of static 2D images, and generate serial cross-sections through 3D structures, is a major step forward, which not only enhances students experience but also nurtures deeper learning. Explaining why on 2D sections upright folds can appear strongly asymmetric, or why a dextral fault can result in an apparent sinistral offset can be a very challenging thing to do. Tools like SketchUp can help make the learning process far more immediate and easier. My collection of 3D SketchUp models is available at: https://3dwarehouse.sketchup.com/user.html?id=1151977671192710697351083 See also interaction 3D model embedded into an eBook: https://itunes.apple.com/au/book/introduction-to-structural/id1085911016?mt=13

Incorporating 3-dimensional models in online articles.

PubMed

Cevidanes, Lucia H S; Ruellas, Antonio C O; Jomier, Julien; Nguyen, Tung; Pieper, Steve; Budin, Francois; Styner, Martin; Paniagua, Beatriz

2015-05-01

The aims of this article are to introduce the capability to view and interact with 3-dimensional (3D) surface models in online publications, and to describe how to prepare surface models for such online 3D visualizations. Three-dimensional image analysis methods include image acquisition, construction of surface models, registration in a common coordinate system, visualization of overlays, and quantification of changes. Cone-beam computed tomography scans were acquired as volumetric images that can be visualized as 3D projected images or used to construct polygonal meshes or surfaces of specific anatomic structures of interest. The anatomic structures of interest in the scans can be labeled with color (3D volumetric label maps), and then the scans are registered in a common coordinate system using a target region as the reference. The registered 3D volumetric label maps can be saved in .obj, .ply, .stl, or .vtk file formats and used for overlays, quantification of differences in each of the 3 planes of space, or color-coded graphic displays of 3D surface distances. All registered 3D surface models in this study were saved in .vtk file format and loaded in the Elsevier 3D viewer. In this study, we describe possible ways to visualize the surface models constructed from cone-beam computed tomography images using 2D and 3D figures. The 3D surface models are available in the article's online version for viewing and downloading using the reader's software of choice. These 3D graphic displays are represented in the print version as 2D snapshots. Overlays and color-coded distance maps can be displayed using the reader's software of choice, allowing graphic assessment of the location and direction of changes or morphologic differences relative to the structure of reference. The interpretation of 3D overlays and quantitative color-coded maps requires basic knowledge of 3D image analysis. When submitting manuscripts, authors can now upload 3D models that will allow readers to interact with or download them. Such interaction with 3D models in online articles now will give readers and authors better understanding and visualization of the results. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

SubductionGenerator: A program to build three-dimensional plate configurations

NASA Astrophysics Data System (ADS)

Jadamec, M. A.; Kreylos, O.; Billen, M. I.; Turcotte, D. L.; Knepley, M.

2016-12-01

Geologic, geochemical, and geophysical data from subduction zones indicate that a two-dimensional paradigm for plate tectonic boundaries is no longer adequate to explain the observations. Many open source software packages exist to simulate the viscous flow of the Earth, such as the dynamics of subduction. However, there are few open source programs that generate the three-dimensional model input. We present an open source software program, SubductionGenerator, that constructs the three-dimensional initial thermal structure and plate boundary structure. A 3D model mesh and tectonic configuration are constructed based on a user specified model domain, slab surface, seafloor age grid file, and shear zone surface. The initial 3D thermal structure for the plates and mantle within the model domain is then constructed using a series of libraries within the code that use a half-space cooling model, plate cooling model, and smoothing functions. The code maps the initial 3D thermal structure and the 3D plate interface onto the mesh nodes using a series of libraries including a k-d tree to increase efficiency. In this way, complicated geometries and multiple plates with variable thickness can be built onto a multi-resolution finite element mesh with a 3D thermal structure and 3D isotropic shear zones oriented at any angle with respect to the grid. SubductionGenerator is aimed at model set-ups more representative of the earth, which can be particularly challenging to construct. Examples include subduction zones where the physical attributes vary in space, such as slab dip and temperature, and overriding plate temperature and thickness. Thus, the program can been used to construct initial tectonic configurations for triple junctions and plate boundary corners.

The Application of COMSOL Multiphysics Package on the Modelling of Complex 3-D Lithospheric Electrical Resistivity Structures - A Case Study from the Proterozoic Orogenic belt within the North China Craton

NASA Astrophysics Data System (ADS)

Guo, L.; Yin, Y.; Deng, M.; Guo, L.; Yan, J.

2017-12-01

At present, most magnetotelluric (MT) forward modelling and inversion codes are based on finite difference method. But its structured mesh gridding cannot be well adapted for the conditions with arbitrary topography or complex tectonic structures. By contrast, the finite element method is more accurate in calculating complex and irregular 3-D region and has lower requirement of function smoothness. However, the complexity of mesh gridding and limitation of computer capacity has been affecting its application. COMSOL Multiphysics is a cross-platform finite element analysis, solver and multiphysics full-coupling simulation software. It achieves highly accurate numerical simulations with high computational performance and outstanding multi-field bi-directional coupling analysis capability. In addition, its AC/DC and RF module can be used to easily calculate the electromagnetic responses of complex geological structures. Using the adaptive unstructured grid, the calculation is much faster. In order to improve the discretization technique of computing area, we use the combination of Matlab and COMSOL Multiphysics to establish a general procedure for calculating the MT responses for arbitrary resistivity models. The calculated responses include the surface electric and magnetic field components, impedance components, magnetic transfer functions and phase tensors. Then, the reliability of this procedure is certificated by 1-D, 2-D and 3-D and anisotropic forward modeling tests. Finally, we establish the 3-D lithospheric resistivity model for the Proterozoic Wutai-Hengshan Mts. within the North China Craton by fitting the real MT data collected there. The reliability of the model is also verified by induced vectors and phase tensors. Our model shows more details and better resolution, compared with the previously published 3-D model based on the finite difference method. In conclusion, COMSOL Multiphysics package is suitable for modeling the 3-D lithospheric resistivity structures under complex tectonic deformation backgrounds, which could be a good complement to the existing finite-difference inversion algorithms.

ModeRNA: a tool for comparative modeling of RNA 3D structure

PubMed Central

Rother, Magdalena; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

2011-01-01

RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available. PMID:21300639

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

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

PubMed

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

2017-07-01

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

Segmentation of 3d Models for Cultural Heritage Structural Analysis - Some Critical Issues

NASA Astrophysics Data System (ADS)

Gonizzi Barsanti, S.; Guidi, G.; De Luca, L.

2017-08-01

Cultural Heritage documentation and preservation has become a fundamental concern in this historical period. 3D modelling offers a perfect aid to record ancient buildings and artefacts and can be used as a valid starting point for restoration, conservation and structural analysis, which can be performed by using Finite Element Methods (FEA). The models derived from reality-based techniques, made up of the exterior surfaces of the objects captured at high resolution, are - for this reason - made of millions of polygons. Such meshes are not directly usable in structural analysis packages and need to be properly pre-processed in order to be transformed in volumetric meshes suitable for FEA. In addition, dealing with ancient objects, a proper segmentation of 3D volumetric models is needed to analyse the behaviour of the structure with the most suitable level of detail for the different sections of the structure under analysis. Segmentation of 3D models is still an open issue, especially when dealing with ancient, complicated and geometrically complex objects that imply the presence of anomalies and gaps, due to environmental agents such as earthquakes, pollution, wind and rain, or human factors. The aims of this paper is to critically analyse some of the different methodologies and algorithms available to segment a 3D point cloud or a mesh, identifying difficulties and problems by showing examples on different structures.

X-ray structure determination at low resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunger, Axel T., E-mail: brunger@stanford.edu; Department of Molecular and Cellular Physiology, Stanford University; Department of Neurology and Neurological Sciences, Stanford University

2009-02-01

Refinement is meaningful even at 4 Å or lower, but with present methodologies it should start from high-resolution crystal structures whenever possible. As an example of structure determination in the 3.5–4.5 Å resolution range, crystal structures of the ATPase p97/VCP, consisting of an N-terminal domain followed by a tandem pair of ATPase domains (D1 and D2), are discussed. The structures were originally solved by molecular replacement with the high-resolution structure of the N-D1 fragment of p97/VCP, whereas the D2 domain was manually built using its homology to the D1 domain as a guide. The structure of the D2 domain alonemore » was subsequently solved at 3 Å resolution. The refined model of D2 and the high-resolution structure of the N-D1 fragment were then used as starting models for re-refinement against the low-resolution diffraction data for full-length p97. The re-refined full-length models showed significant improvement in both secondary structure and R values. The free R values dropped by as much as 5% compared with the original structure refinements, indicating that refinement is meaningful at low resolution and that there is information in the diffraction data even at ∼4 Å resolution that objectively assesses the quality of the model. It is concluded that de novo model building is problematic at low resolution and refinement should start from high-resolution crystal structures whenever possible.« less

Improving Visibility of Stereo-Radiographic Spine Reconstruction with Geometric Inferences.

PubMed

Kumar, Sampath; Nayak, K Prabhakar; Hareesha, K S

2016-04-01

Complex deformities of the spine, like scoliosis, are evaluated more precisely using stereo-radiographic 3D reconstruction techniques. Primarily, it uses six stereo-corresponding points available on the vertebral body for the 3D reconstruction of each vertebra. The wireframe structure obtained in this process has poor visualization, hence difficult to diagnose. In this paper, a novel method is proposed to improve the visibility of this wireframe structure using a deformation of a generic spine model in accordance with the 3D-reconstructed corresponding points. Then, the geometric inferences like vertebral orientations are automatically extracted from the radiographs to improve the visibility of the 3D model. Biplanar radiographs are acquired from five scoliotic subjects on a specifically designed calibration bench. The stereo-corresponding point reconstruction method is used to build six-point wireframe vertebral structures and thus the entire spine model. Using the 3D spine midline and automatically extracted vertebral orientation features, a more realistic 3D spine model is generated. To validate the method, the 3D spine model is back-projected on biplanar radiographs and the error difference is computed. Though, this difference is within the error limits available in the literature, the proposed work is simple and economical. The proposed method does not require more corresponding points and image features to improve the visibility of the model. Hence, it reduces the computational complexity. Expensive 3D digitizer and vertebral CT scan models are also excluded from this study. Thus, the visibility of stereo-corresponding point reconstruction is improved to obtain a low-cost spine model for a better diagnosis of spinal deformities.

Combining 3D structure of real video and synthetic objects

NASA Astrophysics Data System (ADS)

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

1998-04-01

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

3D 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.

Establishing the 3-D finite element solid model of femurs in partial by volume rendering.

PubMed

Zhang, Yinwang; Zhong, Wuxue; Zhu, Haibo; Chen, Yun; Xu, Lingjun; Zhu, Jianmin

2013-01-01

It remains rare to report three-dimensional (3-D) finite element solid model of femurs in partial by volume rendering method, though several methods of femoral 3-D finite element modeling are already available. We aim to analyze the advantages of the modeling method by establishing the 3-D finite element solid model of femurs in partial by volume rendering. A 3-D finite element model of the normal human femurs, made up of three anatomic structures: cortical bone, cancellous bone and pulp cavity, was constructed followed by pretreatment of the CT original image. Moreover, the finite-element analysis was carried on different material properties, three types of materials given for cortical bone, six assigned for cancellous bone, and single for pulp cavity. The established 3-D finite element of femurs contains three anatomical structures: cortical bone, cancellous bone, and pulp cavity. The compressive stress primarily concentrated in the medial surfaces of femur, especially in the calcar femorale. Compared with whole modeling by volume rendering method, the 3-D finite element solid model created in partial is more real and fit for finite element analysis. Copyright © 2013 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

3D Printing of Molecular Models

ERIC Educational Resources Information Center

Gardner, Adam; Olson, Arthur

2016-01-01

Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

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.

A Biomechanical Modeling Guided CBCT Estimation Technique

PubMed Central

Zhang, You; Tehrani, Joubin Nasehi; Wang, Jing

2017-01-01

Two-dimensional-to-three-dimensional (2D-3D) deformation has emerged as a new technique to estimate cone-beam computed tomography (CBCT) images. The technique is based on deforming a prior high-quality 3D CT/CBCT image to form a new CBCT image, guided by limited-view 2D projections. The accuracy of this intensity-based technique, however, is often limited in low-contrast image regions with subtle intensity differences. The solved deformation vector fields (DVFs) can also be biomechanically unrealistic. To address these problems, we have developed a biomechanical modeling guided CBCT estimation technique (Bio-CBCT-est) by combining 2D-3D deformation with finite element analysis (FEA)-based biomechanical modeling of anatomical structures. Specifically, Bio-CBCT-est first extracts the 2D-3D deformation-generated displacement vectors at the high-contrast anatomical structure boundaries. The extracted surface deformation fields are subsequently used as the boundary conditions to drive structure-based FEA to correct and fine-tune the overall deformation fields, especially those at low-contrast regions within the structure. The resulting FEA-corrected deformation fields are then fed back into 2D-3D deformation to form an iterative loop, combining the benefits of intensity-based deformation and biomechanical modeling for CBCT estimation. Using eleven lung cancer patient cases, the accuracy of the Bio-CBCT-est technique has been compared to that of the 2D-3D deformation technique and the traditional CBCT reconstruction techniques. The accuracy was evaluated in the image domain, and also in the DVF domain through clinician-tracked lung landmarks. PMID:27831866

Geometries of geoelectrical structures in central Tibetan Plateau from INDEPTH magnetotelluric data

NASA Astrophysics Data System (ADS)

Vozar, J.; Jones, A. G.; Le Pape, F.

2012-12-01

Magnetotelluric (MT) data collected on N-S profiles crossing the Banggong-Nujiang Suture (BNS), which separates the Qiangtang and Lhasa Terranes in central Tibet, as a part of InterNational DEep Profiling of Tibet and the Himalaya project (INDEPTH) are modeled by 2D, 3D inversion codes and 1D petro-physical package LitMod. The modeling exhibits regional resistive and conductive structures correlated with ShuangHu Suture, Tanggula Mountains and strike-slip faults like BengCo-Jiali fault in the south. The BNS is not manifested in the geoelectrical models as a strong crustal regional structure. The strike direction azimuth of mid and lower crustal structures estimated from horizontal slices from 3D modeling (N110°E) is slightly different from one estimated by 2D strike analysis (N100°E). Orientation of crustal structures is perpendicular to convergence direction in this area. The deepest lower crustal conductors are correlated to areas with maximum Moho depth obtained from satellite gravity data. The anisotropic 2D modeling reveals that lower crustal conductor in Lhasa Terrane is anisotropic. This anisotropy can be interpreted as a proof for crustal channel flow below Lhasa Terrane. But same Lhasa lower crust conductor from isotropic 3D modeling can be interpreted more likely as 3D lower Indian crust structure, located to the east from line 500, than geoelectrical anisotropic crustal flow. From deep electromagnetic sounding, supported by independent integrated petro-physical investigation, we can estimate the next upper-mantle conductive layer at depths from 200 km to 250 km below the Lhasa Terrane and less resistive Tibetan lithosphere below the Qiangtang Terrane with conductive upper-mantle in depths about 120 km.

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

ERIC Educational Resources Information Center

Paukstelis, Paul J.

2018-01-01

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

Using 3D modeling techniques to enhance teaching of difficult anatomical concepts

PubMed Central

Pujol, Sonia; Baldwin, Michael; Nassiri, Joshua; Kikinis, Ron; Shaffer, Kitt

2016-01-01

Rationale and Objectives Anatomy is an essential component of medical education as it is critical for the accurate diagnosis in organs and human systems. The mental representation of the shape and organization of different anatomical structures is a crucial step in the learning process. The purpose of this pilot study is to demonstrate the feasibility and benefits of developing innovative teaching modules for anatomy education of first-year medical students based on 3D reconstructions from actual patient data. Materials and Methods A total of 196 models of anatomical structures from 16 anonymized CT datasets were generated using the 3D Slicer open-source software platform. The models focused on three anatomical areas: the mediastinum, the upper abdomen and the pelvis. Online optional quizzes were offered to first-year medical students to assess their comprehension in the areas of interest. Specific tasks were designed for students to complete using the 3D models. Results Scores of the quizzes confirmed a lack of understanding of 3D spatial relationships of anatomical structures despite standard instruction including dissection. Written task material and qualitative review by students suggested that interaction with 3D models led to a better understanding of the shape and spatial relationships among structures, and helped illustrate anatomical variations from one body to another. Conclusion The study demonstrates the feasibility of one possible approach to the generation of 3D models of the anatomy from actual patient data. The educational materials developed have the potential to supplement the teaching of complex anatomical regions and help demonstrate the anatomic variation among patients. PMID:26897601

Comparative 1D and 3D numerical investigation of open-channel junction flows and energy losses

NASA Astrophysics Data System (ADS)

Luo, Hao; Fytanidis, Dimitrios K.; Schmidt, Arthur R.; García, Marcelo H.

2018-07-01

The complexity of open channel confluences stems from flow mixing, secondary circulation, post-confluence flow separation, contraction and backwater effects. These effects in turn result in a large number of parameters required to adequately quantify the junction induced hydraulic resistance and describe mean flow pattern and turbulent flow structures due to flow merging. The recent development in computing power advances the application of 3D Computational Fluid Dynamics (CFD) codes to visualize and understand the Confluence Hydrodynamic Zone (CHZ). Nevertheless, 1D approaches remain the mainstay in large drainage network or waterway system modeling considering computational efficiency and data availability. This paper presents (i) a modified 1D nonlinear dynamic model; (ii) a fully 3D non-hydrostatic, Reynolds-averaged Navier-Stokes Equations (RANS)-based, Computational Fluid Dynamics (CFD) model; (iii) an analysis of changing confluence hydrodynamics and 3D turbulent flow structure under various controls; (iv) a comparison of flow features (i.e. upstream water depths, energy losses and post-confluence contraction) predicted by 1D and 3D models; and (v) parameterization of 3D flow characteristics in 1D modeling through the computation of correction coefficients associated with contraction, energy and momentum. The present comprehensive 3D numerical investigation highlights the driving mechanisms for junction induced energy losses. Moreover, the comparative 1D and 3D study quantifies the deviation of 1D approximations and associated underlying assumptions from the 'true' resultant flow field. The study may also shed light on improving the accuracy of the 1D large network modeling through the parameterization of the complex 3D feature of the flow field and correction of interior boundary conditions at junctions of larger angles and/or with substantial lateral inflows. Moreover, the enclosed numerical investigations may enhance the understanding of the primary mechanisms contributing to hydraulic structure induced turbulent flow behavior and increased hydraulic resistance.

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

Development of three-dimensional brain arteriovenous malformation model for patient communication and young neurosurgeon education.

PubMed

Dong, Mengqi; Chen, Guangzhong; Qin, Kun; Ding, Xiaowen; Zhou, Dong; Peng, Chao; Zeng, Shaojian; Deng, Xianming

2018-01-15

Rapid prototyping technology is used to fabricate three-dimensional (3D) brain arteriovenous malformation (AVM) models and facilitate presurgical patient communication and medical education for young surgeons. Two intracranial AVM cases were selected for this study. Using 3D CT angiography or 3D rotational angiography images, the brain AVM models were reconstructed on personal computer and the rapid prototyping process was completed using a 3D printer. The size and morphology of the models were compared to brain digital subtraction arteriography of the same patients. 3D brain AVM models were used for preoperative patient communication and young neurosurgeon education. Two brain AVM models were successfully produced. By neurosurgeons' evaluation, the printed models have high fidelity with the actual brain AVM structures of the patients. The patient responded positively toward the brain AVM model specific to himself. Twenty surgical residents from residency programs tested the brain AVM models and provided positive feedback on their usefulness as educational tool and resemblance to real brain AVM structures. Patient-specific 3D printed models of brain AVM can be constructed with high fidelity. 3D printed brain AVM models are proved to be helpful in preoperative patient consultation, surgical planning and resident training.

a Line-Based 3d Roof Model Reconstruction Algorithm: Tin-Merging and Reshaping (tmr)

NASA Astrophysics Data System (ADS)

Rau, J.-Y.

2012-07-01

Three-dimensional building model is one of the major components of a cyber-city and is vital for the realization of 3D GIS applications. In the last decade, the airborne laser scanning (ALS) data is widely used for 3D building model reconstruction and object extraction. Instead, based on 3D roof structural lines, this paper presents a novel algorithm for automatic roof models reconstruction. A line-based roof model reconstruction algorithm, called TIN-Merging and Reshaping (TMR), is proposed. The roof structural line, such as edges, eaves and ridges, can be measured manually from aerial stereo-pair, derived by feature line matching or inferred from ALS data. The originality of the TMR algorithm for 3D roof modelling is to perform geometric analysis and topology reconstruction among those unstructured lines and then reshapes the roof-type using elevation information from the 3D structural lines. For topology reconstruction, a line constrained Delaunay Triangulation algorithm is adopted where the input structural lines act as constraint and their vertex act as input points. Thus, the constructed TINs will not across the structural lines. Later at the stage of Merging, the shared edge between two TINs will be check if the original structural line exists. If not, those two TINs will be merged into a polygon. Iterative checking and merging of any two neighboured TINs/Polygons will result in roof polygons on the horizontal plane. Finally, at the Reshaping stage any two structural lines with fixed height will be used to adjust a planar function for the whole roof polygon. In case ALS data exist, the Reshaping stage can be simplified by adjusting the point cloud within the roof polygon. The proposed scheme reduces the complexity of 3D roof modelling and makes the modelling process easier. Five test datasets provided by ISPRS WG III/4 located at downtown Toronto, Canada and Vaihingen, Germany are used for experiment. The test sites cover high rise buildings and residential area with diverse roof type. For performance evaluation, the adopted roof structural lines are manually measured from the provided stereo-pair. Experimental results indicate a nearly 100% success rate for topology reconstruction was achieved provided that the 3D structural lines can be enclosed as polygons. On the other hand, the success rate at the Reshaping stage is dependent on the complexity of the rooftop structure. Thus, a visual inspection and semi-automatic adjustment of roof-type is suggested and implemented to complete the roof modelling. The results demonstrate that the proposed scheme is robust and reliable with a high degree of completeness, correctness, and quality, even when a group of connected buildings with multiple layers and mixed roof types is processed.

Development of a Top-View Numeric Coding Teaching-Learning Trajectory within an Elementary Grades 3-D Visualization Design Research Project

ERIC Educational Resources Information Center

Sack, Jacqueline J.

2013-01-01

This article explicates the development of top-view numeric coding of 3-D cube structures within a design research project focused on 3-D visualization skills for elementary grades children. It describes children's conceptual development of 3-D cube structures using concrete models, conventional 2-D pictures and abstract top-view numeric…

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

PubMed

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

2013-01-01

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

Software for browsing sectioned images of a dog body and generating a 3D model.

PubMed

Park, Jin Seo; Jung, Yong Wook

2016-01-01

The goals of this study were (1) to provide accessible and instructive browsing software for sectioned images and a portable document format (PDF) file that includes three-dimensional (3D) models of an entire dog body and (2) to develop techniques for segmentation and 3D modeling that would enable an investigator to perform these tasks without the aid of a computer engineer. To achieve these goals, relatively important or large structures in the sectioned images were outlined to generate segmented images. The sectioned and segmented images were then packaged into browsing software. In this software, structures in the sectioned images are shown in detail and in real color. After 3D models were made from the segmented images, the 3D models were exported into a PDF file. In this format, the 3D models could be manipulated freely. The browsing software and PDF file are available for study by students, for lecture for teachers, and for training for clinicians. These files will be helpful for anatomical study by and clinical training of veterinary students and clinicians. Furthermore, these techniques will be useful for researchers who study two-dimensional images and 3D models. © 2015 Wiley Periodicals, Inc.

Direct G-code manipulation for 3D material weaving

NASA Astrophysics Data System (ADS)

Koda, S.; Tanaka, H.

2017-04-01

The process of conventional 3D printing begins by first build a 3D model, then convert to the model to G-code via a slicer software, feed the G-code to the printer, and finally start the printing. The most simple and popular 3D printing technique is Fused Deposition Modeling. However, in this method, the printing path that the printer head can take is restricted by the G-code. Therefore the printed 3D models with complex pattern have structural errors like holes or gaps between the printed material lines. In addition, the structural density and the material's position of the printed model are difficult to control. We realized the G-code editing, Fabrix, for making a more precise and functional printed model with both single and multiple material. The models with different stiffness are fabricated by the controlling the printing density of the filament materials with our method. In addition, the multi-material 3D printing has a possibility to expand the physical properties by the material combination and its G-code editing. These results show the new printing method to provide more creative and functional 3D printing techniques.

Hydrostratigraphic and structural controls on streamflow generation in the Chuska Mountains, Navajo Nation, AZ/NM

NASA Astrophysics Data System (ADS)

Tsinnajinnie, L.; Frisbee, M. D.; Wilson, J. L.

2017-12-01

A conceptual model of hydrostratigraphic and structural influences on 3D streamflow generation processes is tested in the Whiskey Creek watershed located in the Chuska Mountains of the Navajo Nation along the northern NM/AZ border. The role of hydrostratigraphy and structure in groundwater processes has been well studied. However, influences of heterogeneity due to geologic structure and stratigraphy of mountain blocks on 3D streamflow generation has received less attention. Three-dimensional flow in mountainous watersheds, such as Saguache Creek (CO) and Rio Hondo (NM), contributes significant amounts of groundwater from deep circulation to streamflow. This fully 3D conceptual model is fundamentally different than watersheds characterized as 2D, those dominated by surface and shallow subsurface runoff, because 3D watersheds can have much longer flowpaths and mean residence times (up to 1000s of years). In contrast to Saguache Creek (volcanic bedrock) and Rio Hondo (crystalline metamorphic), the bedrock geology of the watersheds draining the Chuska Mountains is primarily comprised of sedimentary bedrock capped by extrusive volcanics. We test this conceptual model using a combination of stream gauging, tritium analyses, and endmember mixing analysis (EMMA) on the general ion chemistry and stable isotope composition of water samples collected in 2013-2016. Springs that emerge from the Chuska Sandstone are tritium dead indicative of a large component of pre-bomb pulse water in discharge and deeper 3D flow. EMMA indicates that most streamflow is generated from groundwater emerging from the Chuska Sandstone. Gaining/losing conditions in Whiskey Creek are strongly related to hydrostratigraphy as evidenced by a transition from gaining conditions largely found in the Chuska Sandstone to losing conditions where the underlying Chinle Formation outcrops. Although tritium in Whiskey Creek suggests 3D interactions are present, hydrostratigraphic and structural controls may limit the occurrence of longer residence times and longer flow paths. Mountainous watersheds similar to the 3D hydrostratigraphic and structurally controlled models will exhibit different responses to perturbations, such as climate change, than watersheds that fit existing 2D and 3D conceptual models.

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

NASA Astrophysics Data System (ADS)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.

Exploration of N-arylpiperazine Binding Sites of D2 Dopaminergic Receptor.

PubMed

Soskic, Vukic; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana

2015-01-01

The crystal structures of the D3 dopamine receptor and several other G-protein coupled receptors (GPCRs) were published in recent times. Those 3D structures are used by us and other scientists as a template for the homology modeling and ligand docking analysis of related GPCRs. Our main scientific interest lies in the field of pharmacologically active N-arylpiperazines that exhibit antipsychotic and/or antidepressant properties, and as such are dopaminergic and serotonergic receptor ligands. In this short review article we are presenting synthesis and biological data on the new N-arylpipereazine as well our results on molecular modeling of the interactions of those N-arylpiperazines with the model of D2 dopamine receptors. To obtain that model the crystal structure of the D3 dopamine receptor was used. Our results show that the N-arylpiperazines binding site consists of two pockets: one is the orthosteric binding site where the N-arylpiperazine part of the ligand is docked and the second is a non-canonical accessory binding site for N-arylpipereazine that is formed by a second extracellular loop (ecl2) of the receptor. Until now, the structure of this receptor region was unresolved in crystal structure analyses of the D3 dopamine receptor. To get a more complete picture of the ligand - receptor interaction, DFT quantum mechanical calculations on N-arylpiperazine were performed and the obtained models were used to examine those interactions.

Pharmacophore Based 3D-QSAR, Virtual Screening and Docking Studies on Novel Series of HDAC Inhibitors with Thiophen Linker as Anticancer Agents.

PubMed

Patel, Preeti; Singh, Avineesh; Patel, Vijay K; Jain, Deepak K; Veerasamy, Ravichandran; Rajak, Harish

2016-01-01

Histone deacetylase (HDAC) inhibitors can reactivate gene expression and inhibit the growth and survival of cancer cells. To identify the important pharmacophoric features and correlate 3Dchemical structure with biological activity using 3D-QSAR and Pharmacophore modeling studies. The pharmacophore hypotheses were developed using e-pharmacophore script and phase module. Pharmacophore hypothesis represents the 3D arrangement of molecular features necessary for activity. A series of 55 compounds with wellassigned HDAC inhibitory activity were used for 3D-QSAR model development. Best 3D-QSAR model, which is a five partial least square (PLS) factor model with good statistics and predictive ability, acquired Q2 (0.7293), R2 (0.9811), cross-validated coefficient rcv 2=0.9807 and R2 pred=0.7147 with low standard deviation (0.0952). Additionally, the selected pharmacophore model DDRRR.419 was used as a 3D query for virtual screening against the ZINC database. In the virtual screening workflow, docking studies (HTVS, SP and XP) were carried out by selecting multiple receptors (PDB ID: 1T69, 1T64, 4LXZ, 4LY1, 3MAX, 2VQQ, 3C10, 1W22). Finally, six compounds were obtained based on high scoring function (dock score -11.2278-10.2222 kcal/mol) and diverse structures. The structure activity correlation was established using virtual screening, docking, energetic based pharmacophore modelling, pharmacophore, atom based 3D QSAR models and their validation. The outcomes of these studies could be further employed for the design of novel HDAC inhibitors for anticancer activity.

Acquisition of a Thermophoresis Instrument for Molecular Association Thermodynamic Studies

DTIC Science & Technology

2015-05-20

using NAMD.27 Crystallographic structures of C3d ( PDB code 1C3D) and C3d-CR2 ( PDB code 3OED) were obtained from the protein data bank ( PDB ).28 Missing...This project is funded by DTRA (Defense Threat Reduction Agency) and aims to develop new multienzyme structures for the controlled destruction of...enable detection. Pharmacophore models were developed based on known C3d-ligand interactions and information from computational analysis of structural

High Cycle Fatigue Prediction for Mistuned Bladed Disks with Fully Coupled Fluid-Structural Interaction

DTIC Science & Technology

2006-06-01

response (time domain) structural vibration model for mistuned rotor bladed disk based on the efficient SNM model has been developed. The vi- bration...airfoil and 3D wing, unsteady vortex shedding of a stationary cylinder, induced vibration of a cylinder, forced vibration of a pitching airfoil, induced... vibration and flutter boundary of 2D NACA 64A010 transonic airfoil, 3D plate wing structural response. The predicted results agree well with benchmark

3D MI-DRAGON: new model for the reconstruction of US FDA drug- target network and theoretical-experimental studies of inhibitors of rasagiline derivatives for AChE.

PubMed

Prado-Prado, Francisco; García-Mera, Xerardo; Escobar, Manuel; Alonso, Nerea; Caamaño, Olga; Yañez, Matilde; González-Díaz, Humberto

2012-01-01

The number of neurodegenerative diseases has been increasing in recent years. Many of the drug candidates to be used in the treatment of neurodegenerative diseases present specific 3D structural features. An important protein in this sense is the acetylcholinesterase (AChE), which is the target of many Alzheimer's dementia drugs. Consequently, the prediction of Drug-Protein Interactions (DPIs/nDPIs) between new drug candidates and specific 3D structure and targets is of major importance. To this end, we can use Quantitative Structure-Activity Relationships (QSAR) models to carry out a rational DPIs prediction. Unfortunately, many previous QSAR models developed to predict DPIs take into consideration only 2D structural information and codify the activity against only one target. To solve this problem we can develop some 3D multi-target QSAR (3D mt-QSAR) models. In this study, using the 3D MI-DRAGON technique, we have introduced a new predictor for DPIs based on two different well-known software. We have used the MARCH-INSIDE (MI) and DRAGON software to calculate 3D structural parameters for drugs and targets respectively. Both classes of 3D parameters were used as input to train Artificial Neuronal Network (ANN) algorithms using as benchmark dataset the complex network (CN) made up of all DPIs between US FDA approved drugs and their targets. The entire dataset was downloaded from the DrugBank database. The best 3D mt-QSAR predictor found was an ANN of Multi-Layer Perceptron-type (MLP) with profile MLP 37:37-24-1:1. This MLP classifies correctly 274 out of 321 DPIs (Sensitivity = 85.35%) and 1041 out of 1190 nDPIs (Specificity = 87.48%), corresponding to training Accuracy = 87.03%. We have validated the model with external predicting series with Sensitivity = 84.16% (542/644 DPIs; Specificity = 87.51% (2039/2330 nDPIs) and Accuracy = 86.78%. The new CNs of DPIs reconstructed from US FDA can be used to explore large DPI databases in order to discover both new drugs and/or targets. We have carried out some theoretical-experimental studies to illustrate the practical use of 3D MI-DRAGON. First, we have reported the prediction and pharmacological assay of 22 different rasagiline derivatives with possible AChE inhibitory activity. In this work, we have reviewed different computational studies on Drug- Protein models. First, we have reviewed 10 studies on DP computational models. Next, we have reviewed 2D QSAR, 3D QSAR, CoMFA, CoMSIA and Docking with different compounds to find Drug-Protein QSAR models. Last, we have developped a 3D multi-target QSAR (3D mt-QSAR) models for the prediction of the activity of new compounds against different targets or the discovery of new targets.

e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures.

PubMed

Solomon, Oz; Eyal, Eran; Amariglio, Ninette; Unger, Ron; Rechavi, Gidi

2016-07-15

e23D, a database of A-to-I RNA editing sites from human, mouse and fly mapped to evolutionary related protein 3D structures, is presented. Genomic coordinates of A-to-I RNA editing sites are converted to protein coordinates and mapped onto 3D structures from PDB or theoretical models from ModBase. e23D allows visualization of the protein structure, modeling of recoding events and orientation of the editing with respect to nearby genomic functional sites from databases of disease causing mutations and genomic polymorphism. http://www.sheba-cancer.org.il/e23D CONTACT: oz.solomon@live.biu.ac.il or Eran.Eyal@sheba.health.gov.il. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Alignment-independent technique for 3D QSAR analysis

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

The virtual dissecting room: Creating highly detailed anatomy models for educational purposes.

PubMed

Zilverschoon, Marijn; Vincken, Koen L; Bleys, Ronald L A W

2017-01-01

Virtual 3D models are powerful tools for teaching anatomy. At the present day, there are a lot of different digital anatomy models, most of these commercial applications are based on a 3D model of a human body reconstructed from images with a 1mm intervals. The use of even smaller intervals may result in more details and more realistic appearances of 3D anatomy models. The aim of this study was to create a realistic and highly detailed 3D model of the hand and wrist based on small interval cross-sectional images, suitable for undergraduate and postgraduate teaching purposes with the possibility to perform a virtual dissection in an educational application. In 115 transverse cross-sections from a human hand and wrist, segmentation was done by manually delineating 90 different structures. With the use of Amira the segments were imported and a surface model/polygon model was created, followed by smoothening of the surfaces in Mudbox. In 3D Coat software the smoothed polygon models were automatically retopologied into a quadrilaterals formation and a UV map was added. In Mudbox, the textures from 90 structures were depicted in a realistic way by using photos from real tissue and afterwards height maps, gloss and specular maps were created to add more level of detail and realistic lightning on every structure. Unity was used to build a new software program that would support all the extra map features together with a preferred user interface. A 3D hand model has been created, containing 100 structures (90 at start and 10 extra structures added along the way). The model can be used interactively by changing the transparency, manipulating single or grouped structures and thereby simulating a virtual dissection. This model can be used for a variety of teaching purposes, ranging from undergraduate medical students to residents of hand surgery. Studying the hand and wrist anatomy using this model is cost-effective and not hampered by the limited access to real dissecting facilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Limits on estimating the width of thin tubular structures in 3D images.

PubMed

Wörz, Stefan; Rohr, Karl

2006-01-01

This work studies limits on estimating the width of thin tubular structures in 3D images. Based on nonlinear estimation theory we analyze the minimal stochastic error of estimating the width. Given a 3D analytic model of the image intensities of tubular structures, we derive a closed-form expression for the Cramér-Rao bound of the width estimate under image noise. We use the derived lower bound as a benchmark and compare it with three previously proposed accuracy limits for vessel width estimation. Moreover, by experimental investigations we demonstrate that the derived lower bound can be achieved by fitting a 3D parametric intensity model directly to the image data.

Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors

NASA Astrophysics Data System (ADS)

Santos-Filho, Osvaldo A.; Mishra, Rama K.; Hopfinger, A. J.

2001-09-01

Free energy force field (FEFF) 3D-QSAR analysis was used to construct ligand-receptor binding models for a set of 18 structurally diverse antifolates including pyrimethamine, cycloguanil, methotrexate, aminopterin and trimethoprim, and 13 pyrrolo[2,3-d]pyrimidines. The molecular target (`receptor') used was a 3D-homology model of a specific mutant type of Plasmodium falciparum (Pf) dihydrofolate reductase (DHFR). The dependent variable of the 3D-QSAR models is the IC50 inhibition constant for the specific mutant type of PfDHFR. The independent variables of the 3D-QSAR models (the descriptors) are scaled energy terms of a modified first-generation AMBER force field combined with a hydration shell aqueous solvation model and a collection of 2D-QSAR descriptors often used in QSAR studies. Multiple temperature molecular dynamics simulation (MDS) and the genetic function approximation (GFA) were employed using partial least square (PLS) and multidimensional linear regressions as the fitting functions to develop FEFF 3D-QSAR models for the binding process. The significant FEFF energy terms in the best 3D-QSAR models include energy contributions of the direct ligand-receptor interaction. Some changes in conformational energy terms of the ligand due to binding to the enzyme are also found to be important descriptors. The FEFF 3D-QSAR models indicate some structural features perhaps relevant to the mechanism of resistance of the PfDHFR to current antimalarials. The FEFF 3D-QSAR models are also compared to receptor-independent (RI) 4D-QSAR models developed in an earlier study and subsequently refined using recently developed generalized alignment rules.

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

NASA Astrophysics Data System (ADS)

Qin, W.; Yang, L.

2004-05-01

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

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

Fundamental limits in 3D landmark localization.

PubMed

Rohr, Karl

2005-01-01

This work analyses the accuracy of estimating the location of 3D landmarks and characteristic image structures. Based on nonlinear estimation theory we study the minimal stochastic errors of the position estimate caused by noisy data. Given analytic models of the image intensities we derive closed-form expressions for the Cramér-Rao bound for different 3D structures such as 3D edges, 3D ridges, 3D lines, and 3D blobs. It turns out, that the precision of localization depends on the noise level, the size of the region-of-interest, the width of the intensity transitions, as well as on other parameters describing the considered image structure. The derived lower bounds can serve as benchmarks and the performance of existing algorithms can be compared with them. To give an impression of the achievable accuracy numeric examples are presented. Moreover, by experimental investigations we demonstrate that the derived lower bounds can be achieved by fitting parametric intensity models directly to the image data.

3D Printing of Biomolecular Models for Research and Pedagogy

PubMed Central

Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

2017-01-01

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. PMID:28362403

A method for mandibular dental arch superimposition using 3D cone beam CT and orthodontic 3D digital model

PubMed Central

Park, Tae-Joon; Lee, Sang-Hyun

2012-01-01

Objective The purpose of this study was to develop superimposition method on the lower arch using 3-dimensional (3D) cone beam computed tomography (CBCT) images and orthodontic 3D digital modeling. Methods Integrated 3D CBCT images were acquired by substituting the dental portion of 3D CBCT images with precise dental images of an orthodontic 3D digital model. Images were acquired before and after treatment. For the superimposition, 2 superimposition methods were designed. Surface superimposition was based on the basal bone structure of the mandible by surface-to-surface matching (best-fit method). Plane superimposition was based on anatomical structures (mental and lingual foramen). For the evaluation, 10 landmarks including teeth and anatomic structures were assigned, and 30 times of superimpositions and measurements were performed to determine the more reproducible and reliable method. Results All landmarks demonstrated that the surface superimposition method produced relatively more consistent coordinate values. The mean distances of measured landmarks values from the means were statistically significantly lower with the surface superimpositions method. Conclusions Between the 2 superimposition methods designed for the evaluation of 3D changes in the lower arch, surface superimposition was the simpler, more reproducible, reliable method. PMID:23112948

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blecic, Jasmina; Dobbs-Dixon, Ian; Greene, Thomas, E-mail: jasmina@nyu.edu

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

Size of graphene sheets determines the structural and mechanical properties of 3D graphene foams

NASA Astrophysics Data System (ADS)

Shen, Zhiqiang; Ye, Huilin; Zhou, Chi; Kröger, Martin; Li, Ying

2018-03-01

Graphene is recognized as an emerging 2D nanomaterial for many applications. Assembly of graphene sheets into 3D structures is an attractive way to enable their macroscopic applications and to preserve the exceptional mechanical and physical properties of their constituents. In this study, we develop a coarse-grained (CG) model for 3D graphene foams (GFs) based on the CG model for a 2D graphene sheet by Ruiz et al (2015 Carbon 82 103-15). We find that the size of graphene sheets plays an important role in both the structural and mechanical properties of 3D GFs. When their size is smaller than 10 nm, the graphene sheets can easily stack together under the influence of van der Waals interactions (vdW). These stacks behave like building blocks and are tightly packed together within 3D GFs, leading to high density, small pore radii, and a large Young’s modulus. However, if the sheet sizes exceed 10 nm, they are staggered together with a significant amount of deformation (bending). Therefore, the density of 3D GFs has been dramatically reduced due to the loosely packed graphene sheets, accompanied by large pore radii and a small Young’s modulus. Under uniaxial compression, rubber-like stress-strain curves are observed for all 3D GFs. This material characteristic is dominated by the vdW interactions between different graphene layers and slightly affected by the out-of-plane deformation of the graphene sheets. We find a simple scaling law E˜ {ρ }4.2 between the density ρ and Young’s modulus E for a model of 3D GFs. The simulation results reveal structure-property relations of 3D GFs, which can be applied to guide the design of 3D graphene assemblies with exceptional properties.

3D-Printed specimens as a valuable tool in anatomy education: A pilot study.

PubMed

Garas, Monique; Vaccarezza, Mauro; Newland, George; McVay-Doornbusch, Kylie; Hasani, Jamila

2018-06-06

Three-dimensional (3D) printing is a modern technique of creating 3D-printed models that allows reproduction of human structures from MRI and CT scans via fusion of multiple layers of resin materials. To assess feasibility of this innovative resource as anatomy educational tool, we conducted a preliminary study on Curtin University undergraduate students to investigate the use of 3D models for anatomy learning as a main goal, to assess the effectiveness of different specimen types during the sessions and personally preferred anatomy learning tools among students as secondary aim. The study consisted of a pre-test, exposure to test (anatomical test) and post-test survey. During pre-test, all participants (both without prior experience and experienced groups) were given a brief introduction on laboratory safety and study procedure thus participants were exposed to 3D, wet and plastinated specimens of the heart, shoulder and thigh to identify the pinned structures (anatomical test). Then, participants were provided a post-test survey containing five questions. In total, 23 participants completed the anatomical test and post-test survey. A larger number of participants (85%) achieved right answers for 3D models compared to wet and plastinated materials, 74% of population selected 3D models as the most usable tool for identification of pinned structures and 45% chose 3D models as their preferred method of anatomy learning. This preliminary small-size study affirms the feasibility of 3D-printed models as a valuable asset in anatomy learning and shows their capability to be used adjacent to cadaveric materials and other widely used tools in anatomy education. Copyright © 2018 Elsevier GmbH. All rights reserved.

G.O.THERM.3D - Providing a 3D Atlas of Temperature in Ireland's Subsurface

NASA Astrophysics Data System (ADS)

Farrell, Thomas; Fullea, Javier

2017-04-01

We introduce the recently initiated project G.O.THERM.3D, which aims to develop a robust and unique model of temperature within Ireland's crust and to produce a 3D temperature atlas of the country. The temperature model will be made publicly available on an interactive online platform, and the project findings will be reported to appropriate state energy and geoscience bodies. The project objective is that an interactive, publicly available 3D temperature model will increase public awareness of geothermal energy. The aim is also that the project findings will focus and encourage geothermal resource exploration and will assist in the development of public policy on geothermal energy exploration, mapping, planning and exploitation. Previous maps of temperature at depth in Ireland's subsurface are heavily reliant on temperature observations in geographically-clustered, shallow boreholes. These maps also make insufficient allowance for near-surface perturbation effects (such as the palaeoclimatic effect), do not allow for the 3D variation of petrophysical parameters and do not consider the deep, lithospheric thermal structure. To develop a 3D temperature model of Ireland's crust, G.O.THERM.3D proposes to model both the compositional and thermal structure of the Irish crust using the LitMod3D geophysical-petrological modelling tool. LitMod3D uses an integrated approach that simultaneously accounts for multiple geophysical (heat-flow, gravity, topography, magnetotelluric, seismic) and petrological (thermal conductivity, heat-production, xenolith composition) datasets, where the main rock properties (density, electrical resistivity, seismic velocity) are thermodynamically computed based on the temperature and bulk rock composition. LitMod3D has been applied to study the lithosphere-asthenosphere boundary (LAB) beneath Ireland (at a depth of 100 km) and is typically used to investigate lithospheric-scale structures. In the previous studies focussing on the LAB beneath Ireland, LitMod3D models the crust as two fixed homogenous layers with laterally constant physical properties (upper-middle crust and lower crust). G.O.THERM.3D proposes to adapt the LitMod3D tool to model the heterogeneous nature of the crust, e.g. the variable distribution of heat production and the variation of thermal conductivity with lithology and temperature, with an appropriate lateral and vertical resolution. The thermal modelling process will also employ palaeoclimate-corrected heat-flow and other available complementary data sets (e.g. seismic, magnetic, radiometric and electromagnetic). Existing and emerging lithospheric-regional temperature models will be used to apply thermal boundary conditions to the crustal model of G.O.THERM.3D. The resulting crustal temperature model of G.O.THERM.3D may in turn be used to provide boundary conditions on more focussed modelling on a shallower scale (e.g. within a sedimentary basin to depths of 5 km). In this way, a nested approach can be adopted to model compositional and thermal structures on various scales and resolutions within the crust (subject to the availability of appropriate data), while maintaining consistency with the wider setting. G.O.THERM.3D will also make additional thermal conductivity measurements, the primary motivation for which being the critical importance of thermal conductivity data in constraining temperature modelling.

Development of the mouse cochlea database (MCD).

PubMed

Santi, Peter A; Rapson, Ian; Voie, Arne

2008-09-01

The mouse cochlea database (MCD) provides an interactive, image database of the mouse cochlea for learning its anatomy and data mining of its resources. The MCD website is hosted on a centrally maintained, high-speed server at the following URL: (http://mousecochlea.umn.edu). The MCD contains two types of image resources, serial 2D image stacks and 3D reconstructions of cochlear structures. Complete image stacks of the cochlea from two different mouse strains were obtained using orthogonal plane fluorescence optical microscopy (OPFOS). 2D images of the cochlea are presented on the MCD website as: viewable images within a stack, 2D atlas of the cochlea, orthogonal sections, and direct volume renderings combined with isosurface reconstructions. In order to assess cochlear structures quantitatively, "true" cross-sections of the scala media along the length of the basilar membrane were generated by virtual resectioning of a cochlea orthogonal to a cochlear structure, such as the centroid of the basilar membrane or the scala media. 3D images are presented on the MCD website as: direct volume renderings, movies, interactive QuickTime VRs, flythrough, and isosurface 3D reconstructions of different cochlear structures. 3D computer models can also be used for solid model fabrication by rapid prototyping and models from different cochleas can be combined to produce an average 3D model. The MCD is the first comprehensive image resource on the mouse cochlea and is a new paradigm for understanding the anatomy of the cochlea, and establishing morphometric parameters of cochlear structures in normal and mutant mice.

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.

Application of Adjoint Method and Spectral-Element Method to Tomographic Inversion of Regional Seismological Structure Beneath Japanese Islands

NASA Astrophysics Data System (ADS)

Tsuboi, S.; Miyoshi, T.; Obayashi, M.; Tono, Y.; Ando, K.

2014-12-01

Recent progress in large scale computing by using waveform modeling technique and high performance computing facility has demonstrated possibilities to perform full-waveform inversion of three dimensional (3D) seismological structure inside the Earth. We apply the adjoint method (Liu and Tromp, 2006) to obtain 3D structure beneath Japanese Islands. First we implemented Spectral-Element Method to K-computer in Kobe, Japan. We have optimized SPECFEM3D_GLOBE (Komatitsch and Tromp, 2002) by using OpenMP so that the code fits hybrid architecture of K-computer. Now we could use 82,134 nodes of K-computer (657,072 cores) to compute synthetic waveform with about 1 sec accuracy for realistic 3D Earth model and its performance was 1.2 PFLOPS. We use this optimized SPECFEM3D_GLOBE code and take one chunk around Japanese Islands from global mesh and compute synthetic seismograms with accuracy of about 10 second. We use GAP-P2 mantle tomography model (Obayashi et al., 2009) as an initial 3D model and use as many broadband seismic stations available in this region as possible to perform inversion. We then use the time windows for body waves and surface waves to compute adjoint sources and calculate adjoint kernels for seismic structure. We have performed several iteration and obtained improved 3D structure beneath Japanese Islands. The result demonstrates that waveform misfits between observed and theoretical seismograms improves as the iteration proceeds. We now prepare to use much shorter period in our synthetic waveform computation and try to obtain seismic structure for basin scale model, such as Kanto basin, where there are dense seismic network and high seismic activity. Acknowledgements: This research was partly supported by MEXT Strategic Program for Innovative Research. We used F-net seismograms of the National Research Institute for Earth Science and Disaster Prevention.

The use of computed tomographic three-dimensional reconstructions to develop instructional models for equine pelvic ultrasonography.

PubMed

Whitcomb, Mary Beth; Doval, John; Peters, Jason

2011-01-01

Ultrasonography has gained increased utility to diagnose pelvic fractures in horses; however, internal pelvic contours can be difficult to appreciate from external palpable landmarks. We developed three-dimensional (3D) simulations of the pelvic ultrasonographic examination to assist with translation of pelvic contours into two-dimensional (2D) images. Contiguous 1mm transverse computed tomography (CT) images were acquired through an equine femur and hemipelvis using a single slice helical scanner. 3D surface models were created using a DICOM reader and imported into a 3D modeling and animation program. The bone models were combined with a purchased 3D horse model and the skin made translucent to visualize pelvic surface contours. 3D models of ultrasound transducers were made from reference photos, and a thin sector shape was created to depict the ultrasound beam. Ultrasonographic examinations were simulated by moving transducers on the skin surface and rectally to produce images of pelvic structures. Camera angles were manipulated to best illustrate the transducer-beam-bone interface. Fractures were created in multiple configurations. Animations were exported as QuickTime movie files for use in presentations coupled with corresponding ultrasound videoclips. 3D models provide a link between ultrasonographic technique and image generation by depicting the interaction of the transducer, ultrasound beam, and structure of interest. The horse model was important to facilitate understanding of the location of pelvic structures relative to the skin surface. While CT acquisition time was brief, manipulation within the 3D software program was time intensive. Results were worthwhile from an instructional standpoint based on user feedback. © 2011 Veterinary Radiology & Ultrasound.

Theoretical limits of localizing 3-D landmarks and features.

PubMed

Rohr, Karl

2007-09-01

In this paper, we analyze the accuracy of estimating the location of 3-D landmarks and characteristic image structures. Based on nonlinear estimation theory, we study the minimal stochastic errors of the position estimate caused by noisy data. Given analytic models of the image intensities, we derive closed-form expressions of the Cramér-Rao bound for different 3-D structures such as 3-D edges, 3-D ridges, 3-D lines, 3-D boxes, and 3-D blobs. It turns out that the precision of localization depends on the noise level, the size of the region-of-interest, the image contrast, the width of the intensity transitions, as well as on other parameters describing the considered image structure. The derived lower bounds can serve as benchmarks and the performance of existing algorithms can be compared with them. To give an impression of the achievable accuracy, numeric examples are presented. Moreover, by experimental investigations, we demonstrate that the derived lower bounds can be achieved by fitting parametric intensity models directly to the image data.

Detailed Anatomy of the Nasolabial Muscle in Human Fetuses as Determined by Micro-CT Combined With Iodine Staining.

PubMed

Wu, Jiajun; Yin, Ningbei

2016-01-01

This study aims to investigate the 3-dimensional (3D) anatomical structure of the orbicularis oris and nasalis, which are closely associated with the appearance of the upper lip and lower part of the nose. The relationship of the complicated 3D anatomical structure with the outline shape was also determined. Microcomputed tomography combined with iodine staining was used to scan the nasolabial tissues of 3 aborted fetuses. The strictly aligned, corrected, full-capacity, 2-dimensional (2D) grayscale images obtained were then used to reconstruct 3D structures using a 3D reconstruction software. 2D grayscale slices and a 3D anatomical model of the orbicularis oris and nasalis of the specimens were obtained. The 2D images and the 3D model confirmed the orbicularis oris anatomical structure reported in previous studies and also provided new insights (such as the close association of the formation of the philtral dimple, lip peak, philtral ridge, and nasal sill with the orbicularis oris). In addition, the results show that the nasolabial muscle consists of muscle fibers from different sources and is divided into four distinct parts: pars marginalis, pars peripheralis, muscle fibers of the levator labii superioris, and nasalis muscle fibers. The 3D anatomical structures indicate that the orbicularis oris and nasalis are closely associated with the appearances of the upper lip and lower part of the nose. The results may aid plastic surgeons in performing cleft-lip correction surgery.

A Simplified Method for the 3D Printing of Molecular Models for Chemical Education

ERIC Educational Resources Information Center

Jones, Oliver A. H.; Spencer, Michelle J. S.

2018-01-01

Using tangible models to help students visualize chemical structures in three dimensions has been a mainstay of chemistry education for many years. Conventional chemistry modeling kits are, however, limited in the types and accuracy of the molecules, bonds and structures they can be used to build. The recent development of 3D printing technology…

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

PubMed

Borrel, Alexandre; Fourches, Denis

2017-12-01

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

Investigation of surface wave amplitudes in 3-D velocity and 3-D Q models

NASA Astrophysics Data System (ADS)

Ruan, Y.; Zhou, Y.

2010-12-01

It has been long recognized that seismic amplitudes depend on both wave speed structures and anelasticity (Q) structures. However, the effects of lateral heterogeneities in wave speed and Q structures on seismic amplitudes has not been well understood. We investigate the effects of 3-D wave speed and 3-D anelasticity (Q) structures on surface-wave amplitudes based upon wave propagation simulations of twelve globally-distributed earthquakes and 801 stations in Earth models with and without lateral heterogeneities in wave speed and anelasticity using a Spectral Element Method (SEM). Our tomographic-like 3-D Q models are converted from a velocity model S20RTS using a set of reasonable mineralogical parameters, assuming lateral perturbations in both velocity and Q are due to temperature perturbations. Surface-wave amplitude variations of SEM seismograms are measured in the period range of 50--200 s using boxcar taper, cosine taper and Slepian multi-tapers. We calculate ray-theoretical predictions of surface-wave amplitude perturbations due to elastic focusing, attenuation, and anelastic focusing which respectively depend upon the second spatial derivative (''roughness'') of perturbations in phase velocity, 1/Q, and the roughness of perturbations in 1/Q. Both numerical experiments and theoretical calculations show that (1) for short-period (~ 50 s) surface waves, the effects of amplitude attenuation due to 3-D Q structures are comparable with elastic focusing effects due to 3-D wave speed structures; and (2) for long-period (> 100 s) surface waves, the effects of attenuation become much weaker than elastic focusing; and (3) elastic focusing effects are correlated with anelastic focusing at all periods due to the correlation between velocity and Q models; and (4) amplitude perturbations are depend on measurement techniques and therefore cannot be directly compared with ray-theoretical predictions because ray theory does not account for the effects of measurement techniques. We calculate 3-D finite-frequency sensitivity of surface-wave amplitude to perturbations in wave speed and anelasticity (Q) which fully account for the effects of elastic focusing, attenuation, anelastic focusing as well as measurement techniques. We show that amplitude perturbations calculated using wave speed and Q sensitivity kernels agree reasonably well with SEM measurements and therefore the sensitivity kernels can be used in a joint inversion of seismic phase delays and amplitudes to simultaneously image high resolution 3-D wave speed and 3-D Q structures in the upper mantle.

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.

SU-C-209-02: 3D Fluoroscopic Image Generation From Patient-Specific 4DCBCT-Based Motion Models Derived From Clinical Patient Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhou, S; Cai, W; Hurwitz, M

Purpose: We develop a method to generate time varying volumetric images (3D fluoroscopic images) using patient-specific motion models derived from four-dimensional cone-beam CT (4DCBCT). Methods: Motion models are derived by selecting one 4DCBCT phase as a reference image, and registering the remaining images to it. Principal component analysis (PCA) is performed on the resultant displacement vector fields (DVFs) to create a reduced set of PCA eigenvectors that capture the majority of respiratory motion. 3D fluoroscopic images are generated by optimizing the weights of the PCA eigenvectors iteratively through comparison of measured cone-beam projections and simulated projections generated from the motionmore » model. This method was applied to images from five lung-cancer patients. The spatial accuracy of this method is evaluated by comparing landmark positions in the 3D fluoroscopic images to manually defined ground truth positions in the patient cone-beam projections. Results: 4DCBCT motion models were shown to accurately generate 3D fluoroscopic images when the patient cone-beam projections contained clearly visible structures moving with respiration (e.g., the diaphragm). When no moving anatomical structure was clearly visible in the projections, the 3D fluoroscopic images generated did not capture breathing deformations, and reverted to the reference image. For the subset of 3D fluoroscopic images generated from projections with visibly moving anatomy, the average tumor localization error and the 95th percentile were 1.6 mm and 3.1 mm respectively. Conclusion: This study showed that 4DCBCT-based 3D fluoroscopic images can accurately capture respiratory deformations in a patient dataset, so long as the cone-beam projections used contain visible structures that move with respiration. For clinical implementation of 3D fluoroscopic imaging for treatment verification, an imaging field of view (FOV) that contains visible structures moving with respiration should be selected. If no other appropriate structures are visible, the images should include the diaphragm. This project was supported, in part, through a Master Research Agreement with Varian Medical Systems, Inc, Palo Alto, CA.« less

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

PubMed

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

2008-12-01

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

Stereoscopic vascular models of the head and neck: A computed tomography angiography visualization.

PubMed

Cui, Dongmei; Lynch, James C; Smith, Andrew D; Wilson, Timothy D; Lehman, Michael N

2016-01-01

Computer-assisted 3D models are used in some medical and allied health science schools; however, they are often limited to online use and 2D flat screen-based imaging. Few schools take advantage of 3D stereoscopic learning tools in anatomy education and clinically relevant anatomical variations when teaching anatomy. A new approach to teaching anatomy includes use of computed tomography angiography (CTA) images of the head and neck to create clinically relevant 3D stereoscopic virtual models. These high resolution images of the arteries can be used in unique and innovative ways to create 3D virtual models of the vasculature as a tool for teaching anatomy. Blood vessel 3D models are presented stereoscopically in a virtual reality environment, can be rotated 360° in all axes, and magnified according to need. In addition, flexible views of internal structures are possible. Images are displayed in a stereoscopic mode, and students view images in a small theater-like classroom while wearing polarized 3D glasses. Reconstructed 3D models enable students to visualize vascular structures with clinically relevant anatomical variations in the head and neck and appreciate spatial relationships among the blood vessels, the skull and the skin. © 2015 American Association of Anatomists.

Complex crustal structures: their 3D grav/mag modelling and 3D printing

NASA Astrophysics Data System (ADS)

Götze, Hans-Jürgen; Schmidt, Sabine; Menzel, Peter

2017-04-01

Our new techniques for modelling and visualization are user-friendly because they are highly interactive, ideally real-time and topology conserving and can be used for both flat and spherical models in 3D. These are important requirements for joint inversion for gravity and magnetic modelling of fields and their derivatives, constrained by seismic and structural input from independent data sources. A borehole tool for magnetic and gravity modelling will also be introduced. We are already close to satisfying the demand of treating several geophysical methods in a single model for subsurface evaluation purposes and aim now for fulfilling most of the constraints: consistency of modelling results and measurements and geological plausibility as well. For 3D modelling, polyhedrons built by triangles are used. All elements of the gravity and magnetic tensors can be included. In the modelling interface, after geometry changes the effect on the model is quickly updated because only the changed triangles have to be recalculated. Because of the triangular model structure, our approach can handle complex structures very well and flexible (e.g. overhangs of salt domes or plumes). For regional models, the use of spherical geometries and calculations is necessary and available. 3D visualization is performed with a 3D-printer (Ultimaker 2) and gives new insights into even rather complicated Earth subsurface structures. Inversion can either be run over the whole model, but typically it is used in smaller parts of the model, helping to solve local problems and/or proving/disproving local hypotheses. The basic principles behind this interactive approach are high performance optimized algorithms (CMA-ES: Covariance-matrix-adoption-evolution-strategy). The efficiency of the algorithm is rather good in terms of stable convergence due to topological model validity. Potential field modelling is always influenced by edge effects. To avoid this, a simple but very robust method has been developed: Derive a density/susceptibility-depth function by taking the mean value of the borders of depth slices through the model. The focus of the presentation is set on two practical examples: From the international KTB - Project, Germanýs deep continental borehole as well as a very complex salt structure in the Northwest German Basin.

A systematic review of clinical value of three-dimensional printing in renal disease.

PubMed

Sun, Zhonghua; Liu, Dongting

2018-04-01

The aim of this systematic review is to analyse current literature related to the clinical value of three-dimensional (3D) printed models in renal disease. A literature search of PubMed and Scopus databases was performed to identify studies reporting the clinical application and usefulness of 3D printed models in renal disease. Fifteen studies were found to meet the selection criteria and were included in the analysis. Eight of them provided quantitative assessments with five studies focusing on dimensional accuracy of 3D printed models in replicating renal anatomy and tumour, and on measuring tumour volume between 3D printed models and original source images and surgical specimens, with mean difference less than 10%. The other three studies reported that the use of 3D printed models significantly enhanced medical students and specialists' ability to identify anatomical structures when compared to two-dimensional (2D) images alone; and significantly shortened intraoperative ultrasound duration compared to without use of 3D printed models. Seven studies provided qualitative assessments of the usefulness of 3D printed kidney models with findings showing that 3D printed models improved patient's understanding of renal anatomy and pathology; improved medical trainees' understanding of renal malignant tumours when compared to viewing medical images alone; and assisted surgical planning and simulation of renal surgical procedures with significant reductions of intraoperative complications. The cost and time associated with 3D printed kidney model production was reported in 10 studies, with costs ranging from USD$100 to USD$1,000, and duration of 3D printing production up to 31 h. The entire process of 3D printing could take up to a few days. This review shows that 3D printed kidney models are accurate in delineating renal anatomical structures and renal tumours with high accuracy. Patient-specific 3D printed models serve as a useful tool in preoperative planning and simulation of surgical procedures for treatment of renal tumours. Further studies with inclusion of more cases and with a focus on reducing the cost and 3D model production time deserve to be investigated.

A systematic review of clinical value of three-dimensional printing in renal disease

PubMed Central

2018-01-01

The aim of this systematic review is to analyse current literature related to the clinical value of three-dimensional (3D) printed models in renal disease. A literature search of PubMed and Scopus databases was performed to identify studies reporting the clinical application and usefulness of 3D printed models in renal disease. Fifteen studies were found to meet the selection criteria and were included in the analysis. Eight of them provided quantitative assessments with five studies focusing on dimensional accuracy of 3D printed models in replicating renal anatomy and tumour, and on measuring tumour volume between 3D printed models and original source images and surgical specimens, with mean difference less than 10%. The other three studies reported that the use of 3D printed models significantly enhanced medical students and specialists’ ability to identify anatomical structures when compared to two-dimensional (2D) images alone; and significantly shortened intraoperative ultrasound duration compared to without use of 3D printed models. Seven studies provided qualitative assessments of the usefulness of 3D printed kidney models with findings showing that 3D printed models improved patient’s understanding of renal anatomy and pathology; improved medical trainees’ understanding of renal malignant tumours when compared to viewing medical images alone; and assisted surgical planning and simulation of renal surgical procedures with significant reductions of intraoperative complications. The cost and time associated with 3D printed kidney model production was reported in 10 studies, with costs ranging from USD$100 to USD$1,000, and duration of 3D printing production up to 31 h. The entire process of 3D printing could take up to a few days. This review shows that 3D printed kidney models are accurate in delineating renal anatomical structures and renal tumours with high accuracy. Patient-specific 3D printed models serve as a useful tool in preoperative planning and simulation of surgical procedures for treatment of renal tumours. Further studies with inclusion of more cases and with a focus on reducing the cost and 3D model production time deserve to be investigated. PMID:29774184

Seismic modeling of Earth's 3D structure: Recent advancements

NASA Astrophysics Data System (ADS)

Ritsema, J.

2008-12-01

Global models of Earth's seismic structure continue to improve due to the growth of seismic data sets, implementation of advanced wave propagations theories, and increased computational power. In my presentation, I will summarize seismic tomography results from the past 5-10 years. I will compare the most recent P and S velocity models, discuss model resolution and model interpretation, and present an, admittedly biased, list of research directions required to develop the next generation 3D models.

Improvement of the Correlative AFM and ToF-SIMS Approach Using an Empirical Sputter Model for 3D Chemical Characterization.

PubMed

Terlier, T; Lee, J; Lee, K; Lee, Y

2018-02-06

Technological progress has spurred the development of increasingly sophisticated analytical devices. The full characterization of structures in terms of sample volume and composition is now highly complex. Here, a highly improved solution for 3D characterization of samples, based on an advanced method for 3D data correction, is proposed. Traditionally, secondary ion mass spectrometry (SIMS) provides the chemical distribution of sample surfaces. Combining successive sputtering with 2D surface projections enables a 3D volume rendering to be generated. However, surface topography can distort the volume rendering by necessitating the projection of a nonflat surface onto a planar image. Moreover, the sputtering is highly dependent on the probed material. Local variation of composition affects the sputter yield and the beam-induced roughness, which in turn alters the 3D render. To circumvent these drawbacks, the correlation of atomic force microscopy (AFM) with SIMS has been proposed in previous studies as a solution for the 3D chemical characterization. To extend the applicability of this approach, we have developed a methodology using AFM-time-of-flight (ToF)-SIMS combined with an empirical sputter model, "dynamic-model-based volume correction", to universally correct 3D structures. First, the simulation of 3D structures highlighted the great advantages of this new approach compared with classical methods. Then, we explored the applicability of this new correction to two types of samples, a patterned metallic multilayer and a diblock copolymer film presenting surface asperities. In both cases, the dynamic-model-based volume correction produced an accurate 3D reconstruction of the sample volume and composition. The combination of AFM-SIMS with the dynamic-model-based volume correction improves the understanding of the surface characteristics. Beyond the useful 3D chemical information provided by dynamic-model-based volume correction, the approach permits us to enhance the correlation of chemical information from spectroscopic techniques with the physical properties obtained by AFM.

3-D Upper-Mantle Shear Velocity Model Beneath the Contiguous United States Based on Broadband Surface Wave from Ambient Seismic Noise

NASA Astrophysics Data System (ADS)

Xie, Jun; Chu, Risheng; Yang, Yingjie

2018-05-01

Ambient noise seismic tomography has been widely used to study crustal and upper-mantle shear velocity structures. Most studies, however, concentrate on short period (< 50 s) surface wave from ambient noise, while studies using long period surface wave from ambient noise are limited. In this paper, we demonstrate the feasibility of using long-period surface wave from ambient noise to study the lithospheric structure on a continental scale. We use broadband Rayleigh wave phase velocities to obtain a 3-D V S structures beneath the contiguous United States at period band of 10-150 s. During the inversion, 1-D shear wave velocity profile is parameterized using B-spline at each grid point and is inverted with nonlinear Markov Chain Monte Carlo method. Then, a 3-D shear velocity model is constructed by assembling all the 1-D shear velocity profiles. Our model is overall consistent with existing models which are based on multiple datasets or data from earthquakes. Our model along with the other post-USArray models reveal lithosphere structures in the upper mantle, which are consistent with the geological tectonic background (e.g., the craton root and regional upwelling provinces). The model has comparable resolution on lithosphere structures compared with many published results and can be used for future detailed regional or continental studies and analysis.

Establishing a National 3d Geo-Data Model for Building Data Compliant to Citygml: Case of Turkey

NASA Astrophysics Data System (ADS)

Ates Aydar, S.; Stoter, J.; Ledoux, H.; Demir Ozbek, E.; Yomralioglu, T.

2016-06-01

This paper presents the generation of the 3D national building geo-data model of Turkey, which is compatible with the international OGC CityGML Encoding Standard. We prepare an ADE named CityGML-TRKBIS.BI that is produced by extending existing thematic modules of CityGML according to TRKBIS needs. All thematic data groups in TRKBIS geo-data model have been remodelled in order to generate the national large scale 3D geo-data model for Turkey. Specific attention has been paid to data groups that have different class structure according to related CityGML data themes such as building data model. Current 2D geo-information model for building data theme of Turkey (TRKBIS.BI) was established based on INSPIRE specifications for building (Core 2D and Extended 2D profiles), ISO/TC 211 standards and OGC web services. New version of TRKBIS.BI which is established according to semantic and geometric rules of CityGML will represent 2D-2.5D and 3D objects. After a short overview on generic approach, this paper describes extending CityGML building data theme according to TRKBIS.BI through several steps. First, building models of both standards were compared according to their data structure, classes and attributes. Second, CityGML building model was extended with respect to TRKBIS needs and CityGML-TRKBIS Building ADE was established in UML. This study provides new insights into 3D applications in Turkey. The generated 3D geo-data model for building thematic class will be used as a common exchange format that meets 2D, 2.5D and 3D implementation needs at national level.

Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models

PubMed Central

Dey, S.

2017-01-01

We present a method to construct and analyse 3D models of underwater scenes using a single cost-effective camera on a standard laptop with (a) free or low-cost software, (b) no computer programming ability, and (c) minimal man hours for both filming and analysis. This study focuses on four key structural complexity metrics: point-to-point distances, linear rugosity (R), fractal dimension (D), and vector dispersion (1/k). We present the first assessment of accuracy and precision of structure-from-motion (SfM) 3D models from an uncalibrated GoPro™ camera at a small scale (4 m2) and show that they can provide meaningful, ecologically relevant results. Models had root mean square errors of 1.48 cm in X-Y and 1.35 in Z, and accuracies of 86.8% (R), 99.6% (D at scales 30–60 cm), 93.6% (D at scales 1–5 cm), and 86.9 (1/k). Values of R were compared to in-situ chain-and-tape measurements, while values of D and 1/k were compared with ground truths from 3D printed objects modelled underwater. All metrics varied less than 3% between independently rendered models. We thereby improve and rigorously validate a tool for ecologists to non-invasively quantify coral reef structural complexity with a variety of multi-scale metrics. PMID:28406937

Application of 3D Laser Scanner to Forensic Engineering.

PubMed

Park, Chan-Seong; Jeon, Hong-Pil; Choi, Kwang-Soo; Kim, Jin-Pyo; Park, Nam-Kyu

2018-05-01

In the case of building collapses and overturned structures, a three-dimensional (3D) collapse or overturn model is required to reconstruct the accident. As construction sites become increasingly complex and large, 3D laser scanning is sometimes the best tool to accurately document and store the site conditions. This case report presents one case of a structure collapse and one case of an overturned crane reconstructed by a 3D laser scanner. In the case of structural collapse of a prefabricated shoring system, a 3D model reconstructed all the members successfully, a task that is nearly impossible using a scale such as a tape measure. The reconstructed prefabricated shoring system was verified through a structural analysis through comparison with the construction drawings to investigate faults in construction. In the case of the overturned crane, the jib angle and other major dimensions were successfully acquired through 3D laser scanning and used to estimate the working radius. As a result, the propriety of the working radius with the given lifting load was successfully determined. © 2017 American Academy of Forensic Sciences.

RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

PubMed

Piatkowski, Pawel; Kasprzak, Joanna M; Kumar, Deepak; Magnus, Marcin; Chojnowski, Grzegorz; Bujnicki, Janusz M

2016-01-01

RNA encompasses an essential part of all known forms of life. The functions of many RNA molecules are dependent on their ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that either utilize information derived from known structures of other RNA molecules (by way of template-based modeling) or attempt to simulate the physical process of RNA structure formation (by way of template-free modeling). All computational methods suffer from various limitations that make theoretical models less reliable than high-resolution experimentally determined structures. This chapter provides a protocol for computational modeling of RNA 3D structure that overcomes major limitations by combining two complementary approaches: template-based modeling that is capable of predicting global architectures based on similarity to other molecules but often fails to predict local unique features, and template-free modeling that can predict the local folding, but is limited to modeling the structure of relatively small molecules. Here, we combine the use of a template-based method ModeRNA with a template-free method SimRNA. ModeRNA requires a sequence alignment of the target RNA sequence to be modeled with a template of the known structure; it generates a model that predicts the structure of a conserved core and provides a starting point for modeling of variable regions. SimRNA can be used to fold small RNAs (<80 nt) without any additional structural information, and to refold parts of models for larger RNAs that have a correctly modeled core. ModeRNA can be either downloaded, compiled and run locally or run through a web interface at http://genesilico.pl/modernaserver/ . SimRNA is currently available to download for local use as a precompiled software package at http://genesilico.pl/software/stand-alone/simrna and as a web server at http://genesilico.pl/SimRNAweb . For model optimization we use QRNAS, available at http://genesilico.pl/qrnas .

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

Ecological connectivity in the three-dimensional urban green volume using waveform airborne lidar

PubMed Central

Casalegno, Stefano; Anderson, Karen; Cox, Daniel T. C.; Hancock, Steven; Gaston, Kevin J.

2017-01-01

The movements of organisms and the resultant flows of ecosystem services are strongly shaped by landscape connectivity. Studies of urban ecosystems have relied on two-dimensional (2D) measures of greenspace structure to calculate connectivity. It is now possible to explore three-dimensional (3D) connectivity in urban vegetation using waveform lidar technology that measures the full 3D structure of the canopy. Making use of this technology, here we evaluate urban greenspace 3D connectivity, taking into account the full vertical stratification of the vegetation. Using three towns in southern England, UK, all with varying greenspace structures, we describe and compare the structural and functional connectivity using both traditional 2D greenspace models and waveform lidar-generated vegetation strata (namely, grass, shrubs and trees). Measures of connectivity derived from 3D greenspace are lower than those derived from 2D models, as the latter assumes that all vertical vegetation strata are connected, which is rarely true. Fragmented landscapes that have more complex 3D vegetation showed greater functional connectivity and we found highest 2D to 3D functional connectivity biases for short dispersal capacities of organisms (6 m to 16 m). These findings are particularly pertinent in urban systems where the distribution of greenspace is critical for delivery of ecosystem services. PMID:28382936

Ecological connectivity in the three-dimensional urban green volume using waveform airborne lidar

NASA Astrophysics Data System (ADS)

Casalegno, Stefano; Anderson, Karen; Cox, Daniel T. C.; Hancock, Steven; Gaston, Kevin J.

2017-04-01

The movements of organisms and the resultant flows of ecosystem services are strongly shaped by landscape connectivity. Studies of urban ecosystems have relied on two-dimensional (2D) measures of greenspace structure to calculate connectivity. It is now possible to explore three-dimensional (3D) connectivity in urban vegetation using waveform lidar technology that measures the full 3D structure of the canopy. Making use of this technology, here we evaluate urban greenspace 3D connectivity, taking into account the full vertical stratification of the vegetation. Using three towns in southern England, UK, all with varying greenspace structures, we describe and compare the structural and functional connectivity using both traditional 2D greenspace models and waveform lidar-generated vegetation strata (namely, grass, shrubs and trees). Measures of connectivity derived from 3D greenspace are lower than those derived from 2D models, as the latter assumes that all vertical vegetation strata are connected, which is rarely true. Fragmented landscapes that have more complex 3D vegetation showed greater functional connectivity and we found highest 2D to 3D functional connectivity biases for short dispersal capacities of organisms (6 m to 16 m). These findings are particularly pertinent in urban systems where the distribution of greenspace is critical for delivery of ecosystem services.

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

PubMed

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

2018-04-23

Three-dimensional (3D) fetal neurosonography is used clinically to detect cerebral abnormalities and to assess growth in the developing brain. However, manual identification of key brain structures in 3D ultrasound images requires expertise to perform and even then is tedious. Inspired by how sonographers view and interact with volumes during real-time clinical scanning, we propose an efficient automatic method to simultaneously localize multiple brain structures in 3D fetal neurosonography. The proposed View-based Projection Networks (VP-Nets), uses three view-based Convolutional Neural Networks (CNNs), to simplify 3D localizations by directly predicting 2D projections of the key structures onto three anatomical views. While designed for efficient use of data and GPU memory, the proposed VP-Nets allows for full-resolution 3D prediction. We investigated parameters that influence the performance of VP-Nets, e.g. depth and number of feature channels. Moreover, we demonstrate that the model can pinpoint the structure in 3D space by visualizing the trained VP-Nets, despite only 2D supervision being provided for a single stream during training. For comparison, we implemented two other baseline solutions based on Random Forest and 3D U-Nets. In the reported experiments, VP-Nets consistently outperformed other methods on localization. To test the importance of loss function, two identical models are trained with binary corss-entropy and dice coefficient loss respectively. Our best VP-Net model achieved prediction center deviation: 1.8 ± 1.4 mm, size difference: 1.9 ± 1.5 mm, and 3D Intersection Over Union (IOU): 63.2 ± 14.7% when compared to the ground truth. To make the whole pipeline intervention free, we also implement a skull-stripping tool using 3D CNN, which achieves high segmentation accuracy. As a result, the proposed processing pipeline takes a raw ultrasound brain image as input, and output a skull-stripped image with five detected key brain structures. Copyright © 2018 Elsevier B.V. All rights reserved.

Edible oil structures at low and intermediate concentrations. II. Ultra-small angle X-ray scattering of in situ tristearin solids in triolein

NASA Astrophysics Data System (ADS)

Peyronel, Fernanda; Ilavsky, Jan; Mazzanti, Gianfranco; Marangoni, Alejandro G.; Pink, David A.

2013-12-01

Ultra-small angle X-ray scattering has been used for the first time to elucidate, in situ, the aggregation structure of a model edible oil system. The three-dimensional nano- to micro-structure of tristearin solid particles in triolein solvent was investigated using 5, 10, 15, and 20% solids. Three different sample preparation procedures were investigated: two slow cooling rates of 0.5°/min, case 1 (22 days of storage at room temperature) and case 2 (no storage), and one fast cooling of 30°/min, case 3 (no storage). The length scale investigated, by using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, Argonne National Laboratory, covered the range from 300 Å to 10 μm. The unified fit and the Guinier-Porod models in the Irena software were used to fit the data. The former was used to fit 3 structural levels. Level 1 structures showed that the primary scatterers were essentially 2-dimensional objects for the three cases. The scatterers possessed lateral dimensions between 1000 and 4300 Å. This is consistent with the sizes of crystalline nanoplatelets present which were observed using cryo-TEM. Level 2 structures were aggregates possessing radii of gyration, Rg2 between 1800 Å and 12000 Å and fractal dimensions of either D2=1 for case 3 or 1.8≤D2≤2.1 for case 1 and case 2. D2 = 1 is consistent with unaggregated 1-dimensional objects. 1.8 ≤ D2 ≤ 2.1 is consistent with these 1-dimensional objects (below) forming structures characteristic of diffusion or reaction limited cluster-cluster aggregation. Level 3 structures showed that the spatial distribution of the level 2 structures was uniform, on the average, for case 1, with fractal dimension D3≈3 while for case 2 and case 3 the fractal dimension was D3≈2.2, which suggested that the large-scale distribution had not come to equilibrium. The Guinier-Porod model showed that the structures giving rise to the aggregates with a fractal dimension given by D2 in the unified fit level 2 model were cylinders described by the parameter s ≈1 in the Guinier-Porod model. The size of the base of these cylinders was in agreement with the cryo-TEM observations as well as with the results of the level 1 unified fit model. By estimating the size of the nanoplatelets and understanding the structures formed via their aggregation, it will be possible to engineer novel lipids systems that embody desired functional characteristics.

Distributed parameter modeling of repeated truss structures

NASA Technical Reports Server (NTRS)

Wang, Han-Ching

1994-01-01

A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.

Integration of 3D geological modeling and gravity surveys for geothermal prospection in an Alpine region

NASA Astrophysics Data System (ADS)

Guglielmetti, L.; Comina, C.; Abdelfettah, Y.; Schill, E.; Mandrone, G.

2013-11-01

Thermal sources are common manifestations of geothermal energy resources in Alpine regions. The up-flow of the fluid is well-known to be often linked to cross-cutting fault zones providing a significant volume of fractures. Since conventional exploration methods are challenging in such areas of high topography and complicated logistics, 3D geological modeling based on structural investigation becomes a useful tool for assessing the overall geology of the investigated sites. Geological modeling alone is, however, less effective if not integrated with deep subsurface investigations that could provide a first order information on geological boundaries and an imaging of geological structures. With this aim, in the present paper the combined use of 3D geological modeling and gravity surveys for geothermal prospection of a hydrothermal area in the western Alps was carried out on two sites located in the Argentera Massif (NW Italy). The geothermal activity of the area is revealed by thermal anomalies with surface evidences, such as hot springs, at temperatures up to 70 °C. Integration of gravity measurements and 3D modeling investigates the potential of this approach in the context of geothermal exploration in Alpine regions where a very complex geological and structural setting is expected. The approach used in the present work is based on the comparison between the observed gravity and the gravity effect of the 3D geological models, in order to enhance local effects related to the geothermal system. It is shown that a correct integration of 3D modeling and detailed geophysical survey could allow a better characterization of geological structures involved in geothermal fluids circulation. Particularly, gravity inversions have successfully delineated the continuity in depth of low density structures, such as faults and fractured bands observed at the surface, and have been of great help in improving the overall geological model.

Three-dimensional brain arteriovenous malformation models for clinical use and resident training.

PubMed

Dong, Mengqi; Chen, Guangzhong; Li, Jianyi; Qin, Kun; Ding, Xiaowen; Peng, Chao; Zhou, Dong; Lin, Xiaofeng

2018-01-01

To fabricate three-dimensional (3D) models of brain arteriovenous malformation (bAVM) and report our experience with customized 3D printed models of patients with bAVM as an educational and clinical tool for patients, doctors, and surgical residents. Using computerized tomography angiography (CTA) or digital subtraction angiography (DSA) images, the rapid prototyping process was completed with specialized software and "in-house" 3D printing service. Intraoperative validation of model fidelity was performed by comparing to DSA images of the same patient during the endovascular treatment process. 3D bAVM models were used for preoperative patient education and consultation, surgical planning, and resident training. 3D printed bAVM models were successful made. By neurosurgeons' evaluation, the printed models precisely replicated the actual bAVM structure of the same patients (n = 7, 97% concordance, range 95%-99% with average of < 2 mm variation). The use of 3D models was associated shorter time for preoperative patient education and consultation, higher acceptable of the procedure for patients and relatives, shorter time between obtaining intraoperative DSA data and the start of endovascular treatment. Thirty surgical residents from residency programs tested the bAVM models and provided feedback on their resemblance to real bAVM structures and the usefulness of printed solid model as an educational tool. Patient-specific 3D printed models of bAVM can be constructed with high fidelity. 3D printed bAVM models were proven to be helpful in preoperative patient consultation, surgical planning, and resident training. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

Coarse-grained modeling of RNA 3D structure.

PubMed

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

2016-07-01

Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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 conductive thermal modelling of the URG and adjacent areas. We show that the Variscan crystalline crustal domains with their different radiogenic heat production influence the regional thermal field, while a thermal blanketing effect due to thick thermally low-conductive sediments causes higher temperatures in the central and northern URG. In contrast, local salt domes result in colder temperatures in parts of the southern URG.

Modelling of MOCVD Reactor: New 3D Approach

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

The Sensitivity of Glacial Isostatic Adjustment in West Antarctica to Lateral Variations in Earth Structure

NASA Astrophysics Data System (ADS)

Nield, G.; Whitehouse, P. L.; Blank, B.; van der Wal, W.; O'Donnell, J. P.; Stuart, G. W.; Lloyd, A. J.; Wiens, D.

2017-12-01

Accurate models of Glacial Isostatic Adjustment (GIA) are required for correcting satellite measurements of ice-mass change and for interpretation of geodetic data at the location of present and former ice sheets. Global models of GIA tend to adopt a 1-D representation of Earth structure, varying in the radial direction only. In some regions rheological parameters may differ significantly from this global average leading to bias in model predictions of present-day deformation, geoid change rates and sea-level change. The advancement of 3-D GIA modelling techniques in recent years has led to improvements in the representation of the Earth via the incorporation of laterally varying structure. This study investigates the influence of 3-D Earth structure on deformation rates in West Antarctica using a finite element GIA model with power-law rheology. We utilise datasets of seismic velocity and temperature for the crust and upper mantle with the aim of determining a data-driven Earth model, and consider the differences when compared to deformation predicted from an equivalent 1-D Earth structure.

Construction of a 3D structural model based on balanced cross sections and borehole data to create a fundament for further geolocial and hydrological simulations

NASA Astrophysics Data System (ADS)

Donndorf, St.; Malz, A.; Kley, J.

2012-04-01

Cross section balancing is a generally accepted method for studying fault zone geometries. We show a method for the construction of structural 3D models of complex fault zones using a combination of gOcad modelling and balanced cross sections. In this work a 3D model of the Schlotheim graben in the Thuringian basin was created from serial, parallel cross sections and existing borehole data. The Thuringian Basin is originally a part of the North German Basin, which was separated from it by the Harz uplift in the Late Cretaceous. It comprises several parallel NW-trending inversion structures. The Schlotheim graben is one example of these inverted graben zones, whose structure poses special challenges to 3D modelling. The fault zone extends 30 km in NW-SE direction and 1 km in NE-SW direction. This project was split into two parts: data management and model building. To manage the fundamental data a central database was created in ESRI's ArcGIS. The development of a scripting interface handles the data exchange between the different steps of modelling. The first step is the pre-processing of the base data in ArcGIS, followed by cross section balancing with Midland Valley's Move software and finally the construction of the 3D model in Paradigm's gOcad. With the specific aim of constructing a 3D model based on cross sections, the functionality of the gOcad software had to be extended. These extensions include pre-processing functions to create a simplified and usable data base for gOcad as well as construction functions to create surfaces based on linearly distributed data and processing functions to create the 3D model from different surfaces. In order to use the model for further geological and hydrological simulations, special requirements apply to the surface properties. The first characteristic of the surfaces should be a quality mesh, which contains triangles with maximized internal angles. To achieve that, an external meshing tool was included in gOcad. The second characteristic is that intersecting lines between two surfaces must be included in both surfaces and share nodes with them. To finish the modelling process 3D balancing was performed to further improve the model quality.

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.

Evaluation of accuracy of synthetic waveforms for subduction-zone earthquakes by using a land-ocean unified 3D structure model

NASA Astrophysics Data System (ADS)

Okamoto, Taro; Takenaka, Hiroshi; Nakamura, Takeshi

2018-06-01

Seismic wave propagation from shallow subduction-zone earthquakes can be strongly affected by 3D heterogeneous structures, such as oceanic water and sedimentary layers with irregular thicknesses. Synthetic waveforms must incorporate these effects so that they reproduce the characteristics of the observed waveforms properly. In this paper, we evaluate the accuracy of synthetic waveforms for small earthquakes in the source area of the 2011 Tohoku-Oki earthquake ( M JMA 9.0) at the Japan Trench. We compute the synthetic waveforms on the basis of a land-ocean unified 3D structure model using our heterogeneity, oceanic layer, and topography finite-difference method. In estimating the source parameters, we apply the first-motion augmented moment tensor (FAMT) method that we have recently proposed to minimize biases due to inappropriate source parameters. We find that, among several estimates, only the FAMT solutions are located very near the plate interface, which demonstrates the importance of using a 3D model for ensuring the self-consistency of the structure model, source position, and source mechanisms. Using several different filter passbands, we find that the full waveforms with periods longer than about 10 s can be reproduced well, while the degree of waveform fitting becomes worse for periods shorter than about 10 s. At periods around 4 s, the initial body waveforms can be modeled, but the later large-amplitude surface waves are difficult to reproduce correctly. The degree of waveform fitting depends on the source location, with better fittings for deep sources near land. We further examine the 3D sensitivity kernels: for the period of 12.8 s, the kernel shows a symmetric pattern with respect to the straight path between the source and the station, while for the period of 6.1 s, a curved pattern is obtained. Also, the range of the sensitive area becomes shallower for the latter case. Such a 3D spatial pattern cannot be predicted by 1D Earth models and indicates the strong effects of 3D heterogeneity on short-period ( ≲ 10s) waveforms. Thus, it would be necessary to consider such 3D effects when improving the structure and source models.

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Development of the Improving Process for the 3D Printed Structure

NASA Astrophysics Data System (ADS)

Takagishi, Kensuke; Umezu, Shinjiro

2017-01-01

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

Development of the Improving Process for the 3D Printed Structure

PubMed Central

Takagishi, Kensuke; Umezu, Shinjiro

2017-01-01

The authors focus on the Fused Deposition Modeling (FDM) 3D printer because the FDM 3D printer can print the utility resin material. It can print with low cost and therefore it is the most suitable for home 3D printer. The FDM 3D printer has the problem that it produces layer grooves on the surface of the 3D printed structure. Therefore the authors developed the 3D-Chemical Melting Finishing (3D-CMF) for removing layer grooves. In this method, a pen-style device is filled with a chemical able to dissolve the materials used for building 3D printed structures. By controlling the behavior of this pen-style device, the convex parts of layer grooves on the surface of the 3D printed structure are dissolved, which, in turn, fills the concave parts. In this study it proves the superiority of the 3D-CMF than conventional processing for the 3D printed structure. It proves utilizing the evaluation of the safety, selectively and stability. It confirms the improving of the 3D-CMF and it is confirmed utilizing the data of the surface roughness precision and the observation of the internal state and the evaluation of the mechanical characteristics. PMID:28054558

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

PubMed

Takagishi, Kensuke; Umezu, Shinjiro

2017-01-05

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

Cardiac 3D Printing and its Future Directions.

PubMed

Vukicevic, Marija; Mosadegh, Bobak; Min, James K; Little, Stephen H

2017-02-01

Three-dimensional (3D) printing is at the crossroads of printer and materials engineering, noninvasive diagnostic imaging, computer-aided design, and structural heart intervention. Cardiovascular applications of this technology development include the use of patient-specific 3D models for medical teaching, exploration of valve and vessel function, surgical and catheter-based procedural planning, and early work in designing and refining the latest innovations in percutaneous structural devices. In this review, we discuss the methods and materials being used for 3D printing today. We discuss the basic principles of clinical image segmentation, including coregistration of multiple imaging datasets to create an anatomic model of interest. With applications in congenital heart disease, coronary artery disease, and surgical and catheter-based structural disease, 3D printing is a new tool that is challenging how we image, plan, and carry out cardiovascular interventions. Copyright © 2017 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Cardiac 3D Printing and Its Future Directions

PubMed Central

Vukicevic, Marija; Mosadegh, Bobak; Min, James K.; Little, Stephen H.

2017-01-01

3D printing is at the crossroads of printer and materials engineering; non-invasive diagnostic imaging; computer aided design (CAD); and structural heart intervention. Cardiovascular applications of this technology development include the use of patient-specific 3D models for medical teaching, exploration of valve and vessel function, surgical and catheter-based procedural planning, and early work in designing and refining the latest innovations in percutaneous structural devices. In this review we discuss the methods and materials being used for 3D printing today. We discuss the basic principles of clinical image segmentation including co-registration of multiple imaging datasets to create an anatomic model of interest. With applications in congenital heart disease, coronary artery disease, and in surgical and catheter-based structural disease – 3D printing is a new tool that is challenging how we image, plan, and carry out cardiovascular interventions. PMID:28183437

Ambient noise adjoint tomography for a linear array in North China

NASA Astrophysics Data System (ADS)

Zhang, C.; Yao, H.; Liu, Q.; Yuan, Y. O.; Zhang, P.; Feng, J.; Fang, L.

2017-12-01

Ambient noise tomography based on dispersion data and ray theory has been widely utilized for imaging crustal structures. In order to improve the inversion accuracy, ambient noise tomography based on the 3D adjoint approach or full waveform inversion has been developed recently, however, the computational cost is tremendous. In this study we present 2D ambient noise adjoint tomography for a linear array in north China with significant computational efficiency compared to 3D ambient noise adjoint tomography. During the preprocessing, we first convert the observed data in 3D media, i.e., surface-wave empirical Green's functions (EGFs) from ambient noise cross-correlation, to the reconstructed EGFs in 2D media using a 3D/2D transformation scheme. Different from the conventional steps of measuring phase dispersion, the 2D adjoint tomography refines 2D shear wave speeds along the profile directly from the reconstructed Rayleigh wave EGFs in the period band 6-35s. With the 2D initial model extracted from the 3D model from traditional ambient noise tomography, adjoint tomography updates the model by minimizing the frequency-dependent Rayleigh wave traveltime misfits between the reconstructed EGFs and synthetic Green function (SGFs) in 2D media generated by the spectral-element method (SEM), with a preconditioned conjugate gradient method. The multitaper traveltime difference measurement is applied in four period bands during the inversion: 20-35s, 15-30s, 10-20s and 6-15s. The recovered model shows more detailed crustal structures with pronounced low velocity anomaly in the mid-lower crust beneath the junction of Taihang Mountains and Yin-Yan Mountains compared with the initial model. This low velocity structure may imply the possible intense crust-mantle interactions, probably associated with the magmatic underplating during the Mesozoic to Cenozoic evolution of the region. To our knowledge, it's first time that ambient noise adjoint tomography is implemented in 2D media. Considering the intensive computational cost and storage of 3D adjoint tomography, this 2D ambient noise adjoint tomography has potential advantages to get high-resolution 2D crustal structures with limited computational resource.

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

NASA Astrophysics Data System (ADS)

Dressel, Ingo; Barckhausen, Udo; Heyde, Ingo

2018-01-01

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

SU-E-J-93: Development of Pre-Contoured Human Model Library in DICOM-RT Format for the Epidemiological Study of the Radiotherapy Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pyakuryal, A; Lee, C; Lee, C

Purpose: Prior to 3D conformal radiation therapy planning, patient anatomy information was mostly limited to 2D beams-eye-view from the conventional simulator. To analyze the outcomes of such treatments for radiation late effects, 3D computational human models are often used in commercial treatment planning systems (TPSs). However, several underlying difficulties such as time-consuming manual delineation procedures of a large number of structures in the model have always limited its applications. Primary objective of this work was to develop a human model library for the epidemiological study by converting 3D-surface model organs to DICOM-RT format (DICOM-RT structure) using an in-house built software.more » We converted the ICRP reference human models to DICOM-RT models, which can be readily adopted for various dose calculations. Methods: MATLAB based code were utilized to convert the contour drawings extracted in text-format from the 3D graphic-tool, Rhinoceros into DICOM-RT structure format for 50 different organs of each model using a 16GB dual-core processor. The conversion periods were measured for each DICOM-RT models, and the reconstructed structure volumes were validated against the original 3D-surface models in the TPS. Ten reference hybrid whole-body models (8-pediatric and 2-adults) were automatically processed to create DICOM-RT computational human model library. Results: Mean contour conversion period was found to be 580 (N=2) and 394.5 (N=8) seconds for 50 organs in the adult and pediatric models respectively. A good agreement for large organs (NRMSD <1.0%) and small organs (NRMSD <7.7%) was also observed between the original volumes and corresponding DICOM-RT structure volumes of the organs. Conclusion: The ICRP reference human models were converted into DICOM-RT format to support the epidemiological study using a large cohort of conventional radiotherapy patients. Due to its DICOM-compatibility, the library may be implemented to many other different applications. We also expect to develop the library by including additional models in future.« less

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.

PubMed

Malo, Marcus; Persson, Ronnie; Svensson, Peder; Luthman, Kristina; Brive, Lars

2013-03-01

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β1 adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D2 receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D2 receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Analysis of 3D Prints by X-ray Computed Microtomography and Terahertz Pulsed Imaging.

PubMed

Markl, Daniel; Zeitler, J Axel; Rasch, Cecilie; Michaelsen, Maria Høtoft; Müllertz, Anette; Rantanen, Jukka; Rades, Thomas; Bøtker, Johan

2017-05-01

A 3D printer was used to realise compartmental dosage forms containing multiple active pharmaceutical ingredient (API) formulations. This work demonstrates the microstructural characterisation of 3D printed solid dosage forms using X-ray computed microtomography (XμCT) and terahertz pulsed imaging (TPI). Printing was performed with either polyvinyl alcohol (PVA) or polylactic acid (PLA). The structures were examined by XμCT and TPI. Liquid self-nanoemulsifying drug delivery system (SNEDDS) formulations containing saquinavir and halofantrine were incorporated into the 3D printed compartmentalised structures and in vitro drug release determined. A clear difference in terms of pore structure between PVA and PLA prints was observed by extracting the porosity (5.5% for PVA and 0.2% for PLA prints), pore length and pore volume from the XμCT data. The print resolution and accuracy was characterised by XμCT and TPI on the basis of the computer-aided design (CAD) models of the dosage form (compartmentalised PVA structures were 7.5 ± 0.75% larger than designed; n = 3). The 3D printer can reproduce specific structures very accurately, whereas the 3D prints can deviate from the designed model. The microstructural information extracted by XμCT and TPI will assist to gain a better understanding about the performance of 3D printed dosage forms.

Three-Dimensional Geologic Framework Model for a Karst Aquifer System, Hasty and Western Grove Quadrangles, Northern Arkansas

USGS Publications Warehouse

Turner, Kenzie J.; Hudson, Mark R.; Murray, Kyle E.; Mott, David N.

2007-01-01

Understanding ground-water flow in a karst aquifer benefits from a detailed conception of the three-dimensional (3D) geologic framework. Traditional two-dimensional products, such as geologic maps, cross-sections, and structure contour maps, convey a mental picture of the area but a stronger conceptualization can be achieved by constructing a digital 3D representation of the stratigraphic and structural geologic features. In this study, a 3D geologic model was created to better understand a karst aquifer system in the Buffalo National River watershed in northern Arkansas. The model was constructed based on data obtained from recent, detailed geologic mapping for the Hasty and Western Grove 7.5-minute quadrangles. The resulting model represents 11 stratigraphic zones of Ordovician, Mississippian, and Pennsylvanian age. As a result of the highly dissected topography, stratigraphic and structural control from geologic contacts and interpreted structure contours were sufficient for effectively modeling the faults and folds in the model area. Combined with recent dye-tracing studies, the 3D framework model is useful for visualizing the various geologic features and for analyzing the potential control they exert on the ground-water flow regime. Evaluation of the model, by comparison to published maps and cross-sections, indicates that the model accurately reproduces both the surface geology and subsurface geologic features of the area.

Modeling and simulation studies of human β3 adrenergic receptor and its interactions with agonists.

PubMed

Sahi, Shakti; Tewatia, Parul; Malik, Balwant K

2012-12-01

β3 adrenergic receptor (β3AR) is known to mediate various pharmacological and physiological effects such as thermogenesis in brown adipocytes, lipolysis in white adipocytes, glucose homeostasis and intestinal smooth muscle relaxation. Several efforts have been made in this field to understand their function and regulation in different human tissues and they have emerged as potential attractive targets in drug discovery for the treatment of diabetes, depression, obesity etc. Although the crystal structures of Bovine Rhodopsin and β2 adrenergic receptor have been resolved, to date there is no three dimensional structural information on β3AR. Our aim in this study was to model 3D structure of β3AR by various molecular modeling and simulation techniques. In this paper, we describe a refined predicted model of β3AR using different algorithms for structure prediction. The structural refinement and minimization of the generated 3D model of β3AR were done by Schrodinger suite 9.1. Docking studies of β3AR model with the known agonists enabled us to identify specific residues, viz, Asp 117, Ser 208, Ser 209, Ser 212, Arg 315, Asn 332, within the β3AR binding pocket, which might play an important role in ligand binding. Receptor ligand interaction studies clearly indicated that these five residues showed strong hydrogen bonding interactions with the ligands. The results have been correlated with the experimental data available. The predicted ligand binding interactions and the simulation studies validate the methods used to predict the 3D-structure.

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

PubMed Central

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

2014-01-01

Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID:24748752

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

PubMed

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

2014-01-01

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

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.

PubMed

Shi, Ya-Zhou; Jin, Lei; Feng, Chen-Jie; Tan, Ya-Lan; Tan, Zhi-Jie

2018-06-01

RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.

D Modelling the Invisible Using Ground Penetrating Radar

NASA Astrophysics Data System (ADS)

Agrafiotis, P.; Lampropoulos, K.; Georgopoulos, A.; Moropoulou, A.

2017-02-01

An interdisciplinary team from the National Technical University of Athens is performing the restoration of the Holy Aedicule, which covers the Tomb of Christ within the Church of the Holy Sepulchre in Jerusalem. The first important task was to geometrically document the monument for the production of the necessary base material on which the structural and material prospection studies would be based. One task of this action was to assess the structural behavior of this edifice in order to support subsequent works. It was imperative that the internal composition of the construction be documented as reliably as possible. To this end several data acquisition techniques were employed, among them ground penetrating radar. Interpretation of these measurements revealed the position of the rock, remnants of the initial cave of the burial of Christ. This paper reports on the methodology employed to construct the 3D model of the rock and introduce it into the 3D model of the whole building, thus enhancing the information about the structure. The conversion of the radargrams to horizontal sections of the rock is explained and the construction of the 3D model and its insertion into the 3D model of the Holy Aedicule is described.

From tissue to silicon to plastic: three-dimensional printing in comparative anatomy and physiology

PubMed Central

Lauridsen, Henrik; Hansen, Kasper; Nørgård, Mathias Ørum; Wang, Tobias; Pedersen, Michael

2016-01-01

Comparative anatomy and physiology are disciplines related to structures and mechanisms in three-dimensional (3D) space. For the past centuries, scientific reports in these fields have relied on written descriptions and two-dimensional (2D) illustrations, but in recent years 3D virtual modelling has entered the scene. However, comprehending complex anatomical structures is hampered by reproduction on flat inherently 2D screens. One way to circumvent this problem is in the production of 3D-printed scale models. We have applied computed tomography and magnetic resonance imaging to produce digital models of animal anatomy well suited to be printed on low-cost 3D printers. In this communication, we report how to apply such technology in comparative anatomy and physiology to aid discovery, description, comprehension and communication, and we seek to inspire fellow researchers in these fields to embrace this emerging technology. PMID:27069653

Modeling and Measurement of 3D Deformation of Scoliotic Spine Using 2D X-ray Images

NASA Astrophysics Data System (ADS)

Li, Hao; Leow, Wee Kheng; Huang, Chao-Hui; Howe, Tet Sen

Scoliosis causes deformations such as twisting and lateral bending of the spine. To correct scoliotic deformation, the extents of 3D spinal deformation need to be measured. This paper studies the modeling and measurement of scoliotic spine based on 3D curve model. Through modeling the spine as a 3D Cosserat rod, the 3D structure of a scoliotic spine can be recovered by obtaining the minimum potential energy registration of the rod to the scoliotic spine in the x-ray image. Test results show that it is possible to obtain accurate 3D reconstruction using only the landmarks in a single view, provided that appropriate boundary conditions and elastic properties are included as constraints.

A New Calibration Method for Commercial RGB-D Sensors.

PubMed

Darwish, Walid; Tang, Shenjun; Li, Wenbin; Chen, Wu

2017-05-24

Commercial RGB-D sensors such as Kinect and Structure Sensors have been widely used in the game industry, where geometric fidelity is not of utmost importance. For applications in which high quality 3D is required, i.e., 3D building models of centimeter‑level accuracy, accurate and reliable calibrations of these sensors are required. This paper presents a new model for calibrating the depth measurements of RGB-D sensors based on the structured light concept. Additionally, a new automatic method is proposed for the calibration of all RGB-D parameters, including internal calibration parameters for all cameras, the baseline between the infrared and RGB cameras, and the depth error model. When compared with traditional calibration methods, this new model shows a significant improvement in depth precision for both near and far ranges.

Efficient 3D porous microstructure reconstruction via Gaussian random field and hybrid optimization.

PubMed

Jiang, Z; Chen, W; Burkhart, C

2013-11-01

Obtaining an accurate three-dimensional (3D) structure of a porous microstructure is important for assessing the material properties based on finite element analysis. Whereas directly obtaining 3D images of the microstructure is impractical under many circumstances, two sets of methods have been developed in literature to generate (reconstruct) 3D microstructure from its 2D images: one characterizes the microstructure based on certain statistical descriptors, typically two-point correlation function and cluster correlation function, and then performs an optimization process to build a 3D structure that matches those statistical descriptors; the other method models the microstructure using stochastic models like a Gaussian random field and generates a 3D structure directly from the function. The former obtains a relatively accurate 3D microstructure, but computationally the optimization process can be very intensive, especially for problems with large image size; the latter generates a 3D microstructure quickly but sacrifices the accuracy due to issues in numerical implementations. A hybrid optimization approach of modelling the 3D porous microstructure of random isotropic two-phase materials is proposed in this paper, which combines the two sets of methods and hence maintains the accuracy of the correlation-based method with improved efficiency. The proposed technique is verified for 3D reconstructions based on silica polymer composite images with different volume fractions. A comparison of the reconstructed microstructures and the optimization histories for both the original correlation-based method and our hybrid approach demonstrates the improved efficiency of the approach. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

3D Numerical Models of the Effect of Diking on the Faulting Pattern at Incipient Continental Rifts and Steady-State Spreading Centers

NASA Astrophysics Data System (ADS)

Tian, X.; Choi, E.; Buck, W. R.

2015-12-01

The offset of faults and related topographic relief varies hugely at both continental rifts and mid-ocean ridges (MORs). In some areas fault offset is measured in 10s of meters while in places marked by core complexes it is measured in 10s of kilometers. Variation in the magma supply is thought to control much of these differences. Magma supply is most usefully described by the ratio (M) between rates of lithospheric extension accommodated by magmatic dike intrusion and that occurring via faulting. 2D models with different values of M successfully explain much of the observed cross-sectional structure seen at rifts and ridges. However, magma supply varies along the axis of extension and the interactions between the tectonics and magmatism are inevitably three-dimensional. We investigate the consequences of this along-axis variation in diking in terms of faulting patterns and the associated structures using a 3D parallel geodynamic modeling code, SNAC. Many observed 3D structural features are reproduced: e.g., abyssal hill, oceanic core complex (OCC), inward fault jump, mass wasting, hourglass-shaped median valley, corrugation and mullion structure. An estimated average value of M = 0.65 is suggested as a boundary value for separating abyssal hills and OCCs formation. Previous inconsistency in the M range for OCC formation between 2D model results (M = 0.3˜0.5) and field observations (M < 0.3 or M > 0.5) is reconciled by the along-ridge coupling between different faulting regimes. We also propose asynchronous faulting-induced tensile failure as a new possibility for explaining corrugations seen on the surface of core complexes. For continental rifts, we will describe a suite of 2D and 3D model calculations with a range of initial lithospheric structures and values of M. In one set of the 2D models we limit the extensional tectonic force and show how this affects the maximum topographic relief produced across the rift. We are also interested in comparing models in which the value of M varies as the rift evolves with observations from real rifts and continental margins. Finally, we plan to show how the faulting pattern in 3D can depend on the distribution of dike opening rate along segments for incipient continental rifts.

PubChem3D: Conformer generation

PubMed Central

2011-01-01

Background PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemical structure similarity at some level. PubChem3D enables similarity of chemical structure 3-D conformers to augment the existing similarity of 2-D chemical structure graphs. It is also desirable to relate theoretical 3-D descriptions of chemical structures to experimental biological activity. As such, it is important to be assured that the theoretical conformer models can reproduce experimentally determined bioactive conformations. In the present study, we investigate the effects of three primary conformer generation parameters (the fragment sampling rate, the energy window size, and force field variant) upon the accuracy of theoretical conformer models, and determined optimal settings for PubChem3D conformer model generation and conformer sampling. Results Using the software package OMEGA from OpenEye Scientific Software, Inc., theoretical 3-D conformer models were generated for 25,972 small-molecule ligands, whose 3-D structures were experimentally determined. Different values for primary conformer generation parameters were systematically tested to find optimal settings. Employing a greater fragment sampling rate than the default did not improve the accuracy of the theoretical conformer model ensembles. An ever increasing energy window did increase the overall average accuracy, with rapid convergence observed at 10 kcal/mol and 15 kcal/mol for model building and torsion search, respectively; however, subsequent study showed that an energy threshold of 25 kcal/mol for torsion search resulted in slightly improved results for larger and more flexible structures. Exclusion of coulomb terms from the 94s variant of the Merck molecular force field (MMFF94s) in the torsion search stage gave more accurate conformer models at lower energy windows. Overall average accuracy of reproduction of bioactive conformations was remarkably linear with respect to both non-hydrogen atom count ("size") and effective rotor count ("flexibility"). Using these as independent variables, a regression equation was developed to predict the RMSD accuracy of a theoretical ensemble to reproduce bioactive conformations. The equation was modified to give a minimum RMSD conformer sampling value to help ensure that 90% of the sampled theoretical models should contain at least one conformer within the RMSD sampling value to a "bioactive" conformation. Conclusion Optimal parameters for conformer generation using OMEGA were explored and determined. An equation was developed that provides an RMSD sampling value to use that is based on the relative accuracy to reproduce bioactive conformations. The optimal conformer generation parameters and RMSD sampling values determined are used by the PubChem3D project to generate theoretical conformer models. PMID:21272340

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

NASA Astrophysics Data System (ADS)

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

Introduction After the Chernobyl Nuclear Power Plant (CNPP) disaster (04.26.1986) a huge amount (over 2000 sq. km) of nuclear wastes appeared within so-called "Cher- nobyl Exclusion Zone" (CEZ). At present there are not enough storage facilities in the Ukraine for safe disposal of nuclear wastes and hazardous chemical wastes. The urgent problem now is safe isolation of these dangerous wastes. According to the developed state program of radioactive waste management, the construction of a na- tional storage facility of nuclear wastes is planned. It is also possible to create regional storage facilities for hazardous chemical wastes. The region of our exploration cov- ers the eastern part of the Korosten Plutone and its slope, reaching the CNPP. 3D Space-Time Surface Imaging of Geophysical Fields. There are only three direct meth- ods of stress field reconstruction in present practice, namely the field investigations based on the large-scale fracturing tests, petrotectonic and optical polarization meth- ods. Unfortunately, all these methods are extremely laborious and need the regular field tests, which is difficult to conduct in the areas of anisotropic rock outcrops. A compilation of magnetic and gravity data covering the CNPP area was carried out as a prelude to an interpretation study. More than thirty map products were generated from magnetic, gravity and geodesy data to prepare the 3D Space-Time Surface Images (3D STSI). Multi-layer topography and geophysic surfaces included: total magnetic intensity, isostatically-corrected Bouguer gravity, aspect and slope, first and second derivatives, vertical and horizontal curvature, histogram characteristics and space cor- relation coefficients between the gradient fields. Many maps shows the first and sec- ond derivatives of the potential fields, with the results of lineament (edge) structure detection superimposed. The lineament or edges of the potential fields are located from maximal gradient in many directions extracted from the total vertical and hori- zontal gradient respectively, both shaded from the 5 northeast to 355 northwest. The dip of multi-layer surfaces indicates the down -"gradient" direction in the fields. The methodology of 3D STSI is based on the analysis of vertical and horizontal anisotropy of gravity and magnetic fields, as well as of multi-layer 3D space-time surface model (3D STSM) of the stress fields. The 3D STSM is multi-layer topology structure of 1 lineaments or gradients (edges) and surfaces calculated by uniform matrices of the geophysical fields. One of the information components of the stress fields character- istics is the aspects and slopes for compressive and tensile stresses. Overlaying of the 3D STSI and lineaments with maps of multi-layer gradients enables to create highly reliable 3D Space-Time Kinematic Model "3D STKM". The analysis of 3D STKM in- cluded: - the space-time reconstruct of forces direction and strain distribution scheme during formation of geological structures and structural paragenesis (lineaments) of potential fields; - predict the real location of expected tectonic dislocations, zones of rock fracturing and disintegration, and mass-stable blocks. Based on these data, the 3D STSM are drawn which reflect the geodynamics of territory development on the ground of paleotectonic reconstruction of successive activity stages having formed the present-day lithosphere. Thus three-dimensional STSM allows to construct an un- mixing geodynamic processes in any interval of fixed space-time in coordinates x, y, t(z). The integrated of the 3D STSM and 3D seismic models enables also to create structural-kinematic and geodynamic maps of the Earth's crust at different depth. As a result, the classification of CNPP areas is performed into zones of compressive and tensile stresses characterized by enhanced permeability of rocks, and zones of consoli- dation with minimal rocks permeability. In addition, the vertically alternating zones of extension and consolidation are identified. These data correlate with results of seismic and mining works. Hydrogeological 3D Model. The hydrogeological 3D Model de- velopment starts from the upper hydrodynamic zone, for which the data are available on hydraulic parameters. After calibration of the upper model elements, the deep part of the model is developed using data about the permeability structure of the crystalline rock massif, obtained from the 3D STSM. The results of analysis and the discrepancy of hydrodynamic regime modeling are used to refine the 3D Model for the rocks per- meability structure. This iterative process of consecutive correlation and refinement of model may be repeated many times. As a result of this technique implementation, the areas of active and very slow water exchange are found, and the system is revealed of vertically alternating zones of enhanced filtration and weak permeability. Based on these data, the sites are pre-selected, which are prospective for subsequently more detailed works on grounding the possibility of nuclear wastes isolation in geological formations. The use of the methodology described above is expedient at the stage of more detailed works, if the corresponding complex is provided of geophysical, hydro- geological, field testing and modeling investigations. Summary Successful testing of 3D STSM technology was carried out starting from 1997 till 1999 by the Ministry of Emergency Situations and Nuclear Safety of Ukraine during the realization of the project "Choosing the favorable geological structures for safe isolation of dangerous nuclear wastes of Chernobyl NPP". The performed works enabled us to draw prelim- inary 3D Space-Time Surface Model, structural-kinematic and geodynamic map of 2 the region understudy. As a result, two regions were selected, which are characterized by existence of geodynamic processes of cooling, thermal shrinkage and structural substance compression of geospace medium. Such regions seem to be the most per- spective for deep burials of nuclear wastes. The first structure is located in rapakivi granites within the eastern side of the Korosten Plutone (near Stanishovka village), 45 km south-west of Chernobyl, the second one - in the same rocks within the north- eastern part of the Korosten Plutone, 80 km west of Chernobyl. Acknowledgements The 3D STSM technology was being developed by Y. Bondarenko. I. Zayonts su- pervised the collecting and interpretation of the geologic and geophysical data. The hydrogeological 3D Model was being developed by V. Shestopalov and Y. Rudenko. This presentation uses data and survey results acquired during project "Choosing the favorable geological structures for safe isolation of dangerous nuclear wastes of Cher- nobyl NPP". 3

Stiffness analysis of glued connection of the timber-concrete structure

NASA Astrophysics Data System (ADS)

Daňková, Jana; Mec, Pavel; Majstríková, Tereza

2016-01-01

This paper presents results of experimental and mathematical analysis of stiffness characteristics of a composite timber-concrete structure. The composite timberconcrete structure presented herein is non-typical compared to similar types of building structures. The interaction between the timber and concrete part of the composite cross-section is not based on metal connecting elements, but it is ensured by a glued-in perforated mesh made of plywood. The paper presents results of experimental and mathematical analysis for material alternatives of the solution of the glued joint. The slip modulus values were determined experimentally. Data obtained from the experiment evaluated by means of regression analysis. Test results were also used as input data for the compilation of a 3D model of a composite structure by means of the 3D finite element model. On the basis of result evaluation, it can be stated that the stress-deformation behaviour at shear loading of this specific timber-concrete composite structure can be affected by the type of glue used. Parameters of the 3D model of both alternative of the structure represent well the behaviour of the composite structure and the model can be used for predicting design parameters of a building structure.

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

PubMed

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

2017-01-01

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

Compilation of 3D global conductivity model of the Earth for space weather applications

NASA Astrophysics Data System (ADS)

Alekseev, Dmitry; Kuvshinov, Alexey; Palshin, Nikolay

2015-07-01

We have compiled a global three-dimensional (3D) conductivity model of the Earth with an ultimate goal to be used for realistic simulation of geomagnetically induced currents (GIC), posing a potential threat to man-made electric systems. Bearing in mind the intrinsic frequency range of the most intense disturbances (magnetospheric substorms) with typical periods ranging from a few minutes to a few hours, the compiled 3D model represents the structure in depth range of 0-100 km, including seawater, sediments, earth crust, and partly the lithosphere/asthenosphere. More explicitly, the model consists of a series of spherical layers, whose vertical and lateral boundaries are established based on available data. To compile a model, global maps of bathymetry, sediment thickness, and upper and lower crust thicknesses as well as lithosphere thickness are utilized. All maps are re-interpolated on a common grid of 0.25×0.25 degree lateral spacing. Once the geometry of different structures is specified, each element of the structure is assigned either a certain conductivity value or conductivity versus depth distribution, according to available laboratory data and conversion laws. A numerical formalism developed for compilation of the model, allows for its further refinement by incorporation of regional 3D conductivity distributions inferred from the real electromagnetic data. So far we included into our model four regional conductivity models, available from recent publications, namely, surface conductance model of Russia, and 3D conductivity models of Fennoscandia, Australia, and northwest of the United States.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

NASA Astrophysics Data System (ADS)

Blenkinsop, Thomas; Ellis, Jennifer

2017-04-01

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

Photogrammetry in 3d Modelling of Human Bone Structures from Radiographs

NASA Astrophysics Data System (ADS)

Hosseinian, S.; Arefi, H.

2017-05-01

Photogrammetry can have great impact on the success of medical processes for diagnosis, treatment and surgeries. Precise 3D models which can be achieved by photogrammetry improve considerably the results of orthopedic surgeries and processes. Usual 3D imaging techniques, computed tomography (CT) and magnetic resonance imaging (MRI), have some limitations such as being used only in non-weight-bearing positions, costs and high radiation dose(for CT) and limitations of MRI for patients with ferromagnetic implants or objects in their bodies. 3D reconstruction of bony structures from biplanar X-ray images is a reliable and accepted alternative for achieving accurate 3D information with low dose radiation in weight-bearing positions. The information can be obtained from multi-view radiographs by using photogrammetry. The primary step for 3D reconstruction of human bone structure from medical X-ray images is calibration which is done by applying principles of photogrammetry. After the calibration step, 3D reconstruction can be done using efficient methods with different levels of automation. Because of the different nature of X-ray images from optical images, there are distinct challenges in medical applications for calibration step of stereoradiography. In this paper, after demonstrating the general steps and principles of 3D reconstruction from X-ray images, a comparison will be done on calibration methods for 3D reconstruction from radiographs and they are assessed from photogrammetry point of view by considering various metrics such as their camera models, calibration objects, accuracy, availability, patient-friendly and cost.

Bioengineered silk scaffolds in 3D tissue modeling with focus on mammary tissues.

PubMed

Maghdouri-White, Yas; Bowlin, Gary L; Lemmon, Christopher A; Dréau, Didier

2016-02-01

In vitro generation of three-dimensional (3D) biological tissues and organ-like structures is a promising strategy to study and closely model complex aspects of the molecular, cellular, and physiological interactions of tissue. In particular, in vitro 3D tissue modeling holds promises to further our understanding of breast development. Indeed, biologically relevant 3D structures that combine mammary cells and engineered matrices have improved our knowledge of mammary tissue growth, organization, and differentiation. Several polymeric biomaterials have been used as scaffolds to engineer 3D mammary tissues. Among those, silk fibroin-based biomaterials have many biologically relevant properties and have been successfully used in multiple medical applications. Here, we review the recent advances in engineered scaffolds with an emphasis on breast-like tissue generation and the benefits of modified silk-based scaffolds. Copyright © 2015 Elsevier B.V. All rights reserved.

Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR

NASA Astrophysics Data System (ADS)

Beger, Richard D.; Buzatu, Dan A.; Wilkes, Jon G.

2002-10-01

A three-dimensional quantitative spectrometric data-activity relationship (3D-QSDAR) modeling technique which uses NMR spectral and structural information that is combined in a 3D-connectivity matrix has been developed. A 3D-connectivity matrix was built by displaying all possible assigned carbon NMR chemical shifts, carbon-to-carbon connections, and distances between the carbons. Two-dimensional 13C-13C COSY and 2D slices from the distance dimension of the 3D-connectivity matrix were used to produce a relationship among the 2D spectral patterns for polychlorinated dibenzofurans, dibenzodioxins, and biphenyls (PCDFs, PCDDs, and PCBs respectively) binding to the aryl hydrocarbon receptor (AhR). We refer to this technique as comparative structural connectivity spectral analysis (CoSCoSA) modeling. All CoSCoSA models were developed using forward multiple linear regression analysis of the predicted 13C NMR structure-connectivity spectral bins. A CoSCoSA model for 26 PCDFs had an explained variance (r2) of 0.93 and an average leave-four-out cross-validated variance (q4 2) of 0.89. A CoSCoSA model for 14 PCDDs produced an r2 of 0.90 and an average leave-two-out cross-validated variance (q2 2) of 0.79. One CoSCoSA model for 12 PCBs gave an r2 of 0.91 and an average q2 2 of 0.80. Another CoSCoSA model for all 52 compounds had an r2 of 0.85 and an average q4 2 of 0.52. Major benefits of CoSCoSA modeling include ease of development since the technique does not use molecular docking routines.

Beyond small molecule SAR – using the dopamine D3 receptor crystal structure to guide drug design

PubMed Central

Keck, Thomas M.; Burzynski, Caitlin; Shi, Lei; Newman, Amy Hauck

2016-01-01

The dopamine D3 receptor is a target of pharmacotherapeutic interest in a variety of neurological disorders including schizophrenia, restless leg syndrome, and drug addiction. The high protein sequence homology between the D3 and D2 receptors has posed a challenge to developing D3 receptor-selective ligands whose behavioral actions can be attributed to D3 receptor engagement, in vivo. However, through primarily small molecule structure-activity relationship (SAR) studies, a variety of chemical scaffolds have been discovered over the past two decades that have resulted in several D3 receptor-selective ligands with high affinity and in vivo activity. Nevertheless, viable clinical candidates remain limited. The recent determination of the high-resolution crystal structure of the D3 receptor has invigorated structure-based drug design, providing refinements to the molecular dynamic models and testable predictions about receptor-ligand interactions. This review will highlight recent preclinical and clinical studies demonstrating potential utility of D3 receptor-selective ligands in the treatment of addiction. In addition, new structure-based rational drug design strategies for D3 receptor-selective ligands that complement traditional small molecule SAR to improve the selectivity and directed efficacy profiles are examined. PMID:24484980

LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design.

PubMed

Munteanu, Cristian R; Pedreira, Nieves; Dorado, Julián; Pazos, Alejandro; Pérez-Montoto, Lázaro G; Ubeira, Florencio M; González-Díaz, Humberto

2014-04-01

Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non-annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH-INSIDE software to calculate the Markov-Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure-Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this predictor in the web server named LECTINPred, freely available at http://bio-aims.udc.es/LECTINPred.php. This web server showed the following goodness-of-fit statistics: Sensitivity=96.7 % (for Ls), Specificity=87.6 % (non-active proteins), and Accuracy=92.5 % (for all proteins), considering altogether both the training and external prediction series. In mode 2, users can carry out an automatic retrieval of protein structures from PDB. We illustrated the use of this server, in operation mode 1, performing a data mining of PDB. We predicted Ls scores for +2000 proteins with unknown function and selected the top-scored ones as possible lectins. In operation mode 2, LECTINPred can also upload 3D structural models generated with structure-prediction tools like LOMETS or PHYRE2. The new Ls are expected to be of relevance as cancer biomarkers or useful in parasite vaccine design. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of composite plates by using mechanics of structure genome and comparison with ANSYS

NASA Astrophysics Data System (ADS)

Zhao, Banghua

Motivated by a recently discovered concept, Structure Genome (SG) which is defined as the smallest mathematical building block of a structure, a new approach named Mechanics of Structure Genome (MSG) to model and analyze composite plates is introduced. MSG is implemented in a general-purpose code named SwiftComp(TM), which provides the constitutive models needed in structural analysis by homogenization and pointwise local fields by dehomogenization. To improve the user friendliness of SwiftComp(TM), a simple graphic user interface (GUI) based on ANSYS Mechanical APDL platform, called ANSYS-SwiftComp GUI is developed, which provides a convenient way to create some common SG models or arbitrary customized SG models in ANSYS and invoke SwiftComp(TM) to perform homogenization and dehomogenization. The global structural analysis can also be handled in ANSYS after homogenization, which could predict the global behavior and provide needed inputs for dehomogenization. To demonstrate the accuracy and efficiency of the MSG approach, several numerical cases are studied and compared using both MSG and ANSYS. In the ANSYS approach, 3D solid element models (ANSYS 3D approach) are used as reference models and the 2D shell element models created by ANSYS Composite PrepPost (ACP approach) are compared with the MSG approach. The results of the MSG approach agree well with the ANSYS 3D approach while being as efficient as the ACP approach. Therefore, the MSG approach provides an efficient and accurate new way to model composite plates.

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

PubMed Central

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

2009-01-01

Background: Given the increasing number of indications for liver surgery and the growing complexity of operations, many trainees in surgical, imaging and related subspecialties require a good working knowledge of the complex intrahepatic anatomy. Computed tomography (CT), the most commonly used liver imaging modality, enhances our understanding of liver anatomy, but comprises a two-dimensional (2D) representation of a complex 3D organ. It is challenging for trainees to acquire the necessary skills for converting these 2D images into 3D mental reconstructions because learning opportunities are limited and internal hepatic anatomy is complicated, asymmetrical and variable. We have created a website that uses interactive 3D models of the liver to assist trainees in understanding the complex spatial anatomy of the liver and to help them create a 3D mental interpretation of this anatomy when viewing CT scans. Methods: Computed tomography scans were imported into DICOM imaging software (OsiriX™) to obtain 3D surface renderings of the liver and its internal structures. Using these 3D renderings as a reference, 3D models of the liver surface and the intrahepatic structures, portal veins, hepatic veins, hepatic arteries and the biliary system were created using 3D modelling software (Cinema 4D™). Results: Using current best practices for creating multimedia tools, a unique, freely available, online learning resource has been developed, entitled Visual Interactive Resource for Teaching, Understanding And Learning Liver Anatomy (VIRTUAL Liver) (http://pie.med.utoronto.ca/VLiver). This website uses interactive 3D models to provide trainees with a constructive resource for learning common liver anatomy and liver segmentation, and facilitates the development of the skills required to mentally reconstruct a 3D version of this anatomy from 2D CT scans. Discussion: Although the intended audience for VIRTUAL Liver consists of residents in various medical and surgical specialties, the website will also be useful for other health care professionals (i.e. radiologists, nurses, hepatologists, radiation oncologists, family doctors) and educators because it provides a comprehensive resource for teaching liver anatomy. PMID:19816618

2D-QSAR and 3D-QSAR Analyses for EGFR Inhibitors

PubMed Central

Zhao, Manman; Zheng, Linfeng; Qiu, Chun

2017-01-01

Epidermal growth factor receptor (EGFR) is an important target for cancer therapy. In this study, EGFR inhibitors were investigated to build a two-dimensional quantitative structure-activity relationship (2D-QSAR) model and a three-dimensional quantitative structure-activity relationship (3D-QSAR) model. In the 2D-QSAR model, the support vector machine (SVM) classifier combined with the feature selection method was applied to predict whether a compound was an EGFR inhibitor. As a result, the prediction accuracy of the 2D-QSAR model was 98.99% by using tenfold cross-validation test and 97.67% by using independent set test. Then, in the 3D-QSAR model, the model with q2 = 0.565 (cross-validated correlation coefficient) and r2 = 0.888 (non-cross-validated correlation coefficient) was built to predict the activity of EGFR inhibitors. The mean absolute error (MAE) of the training set and test set was 0.308 log units and 0.526 log units, respectively. In addition, molecular docking was also employed to investigate the interaction between EGFR inhibitors and EGFR. PMID:28630865

Comparison of Commercial Structure-From Photogrammety Software Used for Underwater Three-Dimensional Modeling of Coral Reef Environments

NASA Astrophysics Data System (ADS)

Burns, J. H. R.; Delparte, D.

2017-02-01

Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

Identification of four Aconitum species used as "Caowu" in herbal markets by 3D reconstruction and microstructural comparison.

PubMed

Liu, Chan-Chan; Cheng, Ming-En; Peng, Huasheng; Duan, Hai-Yan; Huang, Luqi

2015-05-01

Authentication is the first priority when evaluating the quality of Chinese herbal medicines, particularly highly toxic medicines. The most commonly used authentication methods are morphological identification and microscopic identification. Unfortunately, these methods could not effectively evaluate some herbs with complex interior structures, such as root of Aconitum species with a circular conical shape and an interior structure with successive changes. Defining the part that should be selected as the standard plays an essential role in accurate microscopic identification. In this study, we first present a visual 3D model of Aconitum carmichaeli Debx. constructed obtained from microscopic analysis of serial sections. Based on this model, we concluded that the point of largest root diameter should be used as the standard for comparison and identification. The interior structure at this point is reproducible and its shape and appearance can easily be used to distinguish among species. We also report details of the interior structures of parts not shown in the 3D model, such as stone cells and cortical thickness. To demonstrate the usefulness of the results from the 3D model, we have distinguished the microscopic structures, at their largest segments, of the other three Aconitum species used for local habitat species of Caowu. This work provides the basis for resolution of some debate regarding the microstructural differences among these species. Thus, we conclude that the 3D model composed of serial sections has enabled the selection of a standard cross-section that will enable the accurate identification of Aconitum species in Chinese medicine. © 2015 Wiley Periodicals, Inc.

A neurosurgical simulation of skull base tumors using a 3D printed rapid prototyping model containing mesh structures.

PubMed

Kondo, Kosuke; Harada, Naoyuki; Masuda, Hiroyuki; Sugo, Nobuo; Terazono, Sayaka; Okonogi, Shinichi; Sakaeyama, Yuki; Fuchinoue, Yutaka; Ando, Syunpei; Fukushima, Daisuke; Nomoto, Jun; Nemoto, Masaaki

2016-06-01

Deep regions are not visible in three-dimensional (3D) printed rapid prototyping (RP) models prepared from opaque materials, which is not the case with translucent images. The objectives of this study were to develop an RP model in which a skull base tumor was simulated using mesh, and to investigate its usefulness for surgical simulations by evaluating the visibility of its deep regions. A 3D printer that employs binder jetting and is mainly used to prepare plaster models was used. RP models containing a solid tumor, no tumor, and a mesh tumor were prepared based on computed tomography, magnetic resonance imaging, and angiographic data for four cases of petroclival tumor. Twelve neurosurgeons graded the three types of RP model into the following four categories: 'clearly visible,' 'visible,' 'difficult to see,' and 'invisible,' based on the visibility of the internal carotid artery, basilar artery, and brain stem through a craniotomy performed via the combined transpetrosal approach. In addition, the 3D positional relationships between these structures and the tumor were assessed. The internal carotid artery, basilar artery, and brain stem and the positional relationships of these structures with the tumor were significantly more visible in the RP models with mesh tumors than in the RP models with solid or no tumors. The deep regions of PR models containing mesh skull base tumors were easy to visualize. This 3D printing-based method might be applicable to various surgical simulations.

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

PubMed

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

2013-04-01

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

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

PubMed Central

Barone, Sandro; Paoli, Alessandro; Razionale, Armando Viviano

2013-01-01

In the field of dental health care, plaster models combined with 2D radiographs are widely used in clinical practice for orthodontic diagnoses. However, complex malocclusions can be better analyzed by exploiting 3D digital dental models, which allow virtual simulations and treatment planning processes. In this paper, dental data captured by independent imaging sensors are fused to create multi-body orthodontic models composed of teeth, oral soft tissues and alveolar bone structures. The methodology is based on integrating Cone-Beam Computed Tomography (CBCT) and surface structured light scanning. The optical scanner is used to reconstruct tooth crowns and soft tissues (visible surfaces) through the digitalization of both patients' mouth impressions and plaster casts. These data are also used to guide the segmentation of internal dental tissues by processing CBCT data sets. The 3D individual dental tissues obtained by the optical scanner and the CBCT sensor are fused within multi-body orthodontic models without human supervisions to identify target anatomical structures. The final multi-body models represent valuable virtual platforms to clinical diagnostic and treatment planning. PMID:23385416

Creation of 3D multi-body orthodontic models by using independent imaging sensors.

PubMed

Barone, Sandro; Paoli, Alessandro; Razionale, Armando Viviano

2013-02-05

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

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

NASA Astrophysics Data System (ADS)

Zamyadi, A.; Pouliot, J.; Bédard, Y.

2013-09-01

Accessing 3D geospatial models, eventually at no cost and for unrestricted use, is certainly an important issue as they become popular among participatory communities, consultants, and officials. Various geo-portals, mainly established for 2D resources, have tried to provide access to existing 3D resources such as digital elevation model, LIDAR or classic topographic data. Describing the content of data, metadata is a key component of data discovery in geo-portals. An inventory of seven online geo-portals and commercial catalogues shows that the metadata referring to 3D information is very different from one geo-portal to another as well as for similar 3D resources in the same geo-portal. The inventory considered 971 data resources affiliated with elevation. 51% of them were from three geo-portals running at Canadian federal and municipal levels whose metadata resources did not consider 3D model by any definition. Regarding the remaining 49% which refer to 3D models, different definition of terms and metadata were found, resulting in confusion and misinterpretation. The overall assessment of these geo-portals clearly shows that the provided metadata do not integrate specific and common information about 3D geospatial models. Accordingly, the main objective of this research is to improve 3D geospatial model discovery in geo-portals by adding a specific metadata-set. Based on the knowledge and current practices on 3D modeling, and 3D data acquisition and management, a set of metadata is proposed to increase its suitability for 3D geospatial models. This metadata-set enables the definition of genuine classes, fields, and code-lists for a 3D metadata profile. The main structure of the proposal contains 21 metadata classes. These classes are classified in three packages as General and Complementary on contextual and structural information, and Availability on the transition from storage to delivery format. The proposed metadata set is compared with Canadian Geospatial Data Infrastructure (CGDI) metadata which is an implementation of North American Profile of ISO-19115. The comparison analyzes the two metadata against three simulated scenarios about discovering needed 3D geo-spatial datasets. Considering specific metadata about 3D geospatial models, the proposed metadata-set has six additional classes on geometric dimension, level of detail, geometric modeling, topology, and appearance information. In addition classes on data acquisition, preparation, and modeling, and physical availability have been specialized for 3D geospatial models.

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

PubMed Central

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

2013-01-01

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

Static reservoir modeling of the Bahariya reservoirs for the oilfields development in South Umbarka area, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Abdel-Fattah, Mohamed I.; Metwalli, Farouk I.; Mesilhi, El Sayed I.

2018-02-01

3D static reservoir modeling of the Bahariya reservoirs using seismic and wells data can be a relevant part of an overall strategy for the oilfields development in South Umbarka area (Western Desert, Egypt). The seismic data is used to build the 3D grid, including fault sticks for the fault modeling, and horizon interpretations and surfaces for horizon modeling. The 3D grid is the digital representation of the structural geology of Bahariya Formation. When we got a reasonably accurate representation, we fill the 3D grid with facies and petrophysical properties to simulate it, to gain a more precise understanding of the reservoir properties behavior. Sequential Indicator Simulation (SIS) and Sequential Gaussian Simulation (SGS) techniques are the stochastic algorithms used to spatially distribute discrete reservoir properties (facies) and continuous reservoir properties (shale volume, porosity, and water saturation) respectively within the created 3D grid throughout property modeling. The structural model of Bahariya Formation exhibits the trapping mechanism which is a fault assisted anticlinal closure trending NW-SE. This major fault breaks the reservoirs into two major fault blocks (North Block and South Block). Petrophysical models classified Lower Bahariya reservoir as a moderate to good reservoir rather than Upper Bahariya reservoir in terms of facies, with good porosity and permeability, low water saturation, and moderate net to gross. The Original Oil In Place (OOIP) values of modeled Bahariya reservoirs show hydrocarbon accumulation in economic quantity, considering the high structural dips at the central part of South Umbarka area. The powerful of 3D static modeling technique has provided a considerable insight into the future prediction of Bahariya reservoirs performance and production behavior.

Application of 3D Laser Scanning Technology in Complex Rock Foundation Design

NASA Astrophysics Data System (ADS)

Junjie, Ma; Dan, Lu; Zhilong, Liu

2017-12-01

Taking the complex landform of Tanxi Mountain Landscape Bridge as an example, the application of 3D laser scanning technology in the mapping of complex rock foundations is studied in this paper. A set of 3D laser scanning technologies are formed and several key engineering problems are solved. The first is 3D laser scanning technology of complex landforms. 3D laser scanning technology is used to obtain a complete 3D point cloud data model of the complex landform. The detailed and accurate results of the surveying and mapping decrease the measuring time and supplementary measuring times. The second is 3D collaborative modeling of the complex landform. A 3D model of the complex landform is established based on the 3D point cloud data model. The super-structural foundation model is introduced for 3D collaborative design. The optimal design plan is selected and the construction progress is accelerated. And the last is finite-element analysis technology of the complex landform foundation. A 3D model of the complex landform is introduced into ANSYS for building a finite element model to calculate anti-slide stability of the rock, and provides a basis for the landform foundation design and construction.

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

NASA Astrophysics Data System (ADS)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

NoSQL Based 3D City Model Management System

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

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

PubMed

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

2012-01-10

This work presents a validation of a fluid-structure interaction computational model simulating the flow conditions in an in vitro mock heart chamber modeling mitral valve regurgitation during the ejection phase during which the trans-valvular pressure drop and valve displacement are not as large. The mock heart chamber was developed to study the use of 2D and 3D color Doppler techniques in imaging the clinically relevant complex intra-cardiac flow events associated with mitral regurgitation. Computational models are expected to play an important role in supporting, refining, and reinforcing the emerging 3D echocardiographic applications. We have developed a 3D computational fluid-structure interaction algorithm based on a semi-implicit, monolithic method, combined with an arbitrary Lagrangian-Eulerian approach to capture the fluid domain motion. The mock regurgitant mitral valve corresponding to an elastic plate with a geometric orifice, was modeled using 3D elasticity, while the blood flow was modeled using the 3D Navier-Stokes equations for an incompressible, viscous fluid. The two are coupled via the kinematic and dynamic conditions describing the two-way coupling. The pressure, the flow rate, and orifice plate displacement were measured and compared with numerical simulation results. In-line flow meter was used to measure the flow, pressure transducers were used to measure the pressure, and a Doppler method developed by one of the authors was used to measure the axial displacement of the orifice plate. The maximum recorded difference between experiment and numerical simulation for the flow rate was 4%, the pressure 3.6%, and for the orifice displacement 15%, showing excellent agreement between the two. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

The 3D geological model of the 1963 Vajont rockslide, reconstructed with implicit surface methods

NASA Astrophysics Data System (ADS)

Bistacchi, Andrea; Massironi, Matteo; Francese, Roberto; Giorgi, Massimo; Taller, Claudio

2015-04-01

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

The 3D structures of G-quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase.

PubMed

Li, Ming-Hui; Zhou, Yi-Han; Luo, Quan; Li, Ze-Sheng

2010-04-01

The unimolecular G-quadruplex structures of d(GGGTGGGTGGGTGGGT) (G1) and d(GTGGTGGGTGGGTGGGT) (G2) are known as the potent nanomolar HIV-1 integrase inhibitors, thus investigating the 3D structures of the two sequences is significant for structure-based rational anti-HIV drug design. In this research, based on the experimental data of circular dichroism (CD) spectropolarimetry and electrospray ionization mass spectrometry (ESI-MS), the initial models of G1 and G2 were constructed by molecular modeling method. The modeling structures of G1 and G2 are intramolecular parallel-stranded quadruplex conformation with three guanine tetrads. Particularly, the structure of G2 possesses a T loop residue between the first and the second G residues that are the component of two adjacent same-stranded G-tetrad planes. This structure proposed by us has a very novel geometry and is different from all reported G-quadruplexes. The extended (35 ns) molecular dynamic (MD) simulations for the models indicate that the G-quadruplexes maintain their structures very well in aqueous solution whether the existence of K(+) or NH (4) (+) in the central channel. Furthermore, we perform 500 ns MD simulations for the models in the gas phase. The results show that all the ion-G-quadruplex complexes are maintained during the whole simulations, despite the large magnitude of phosphate-phosphate repulsions. The gas phase MD simulations provide a good explanation to ESI-MS experiments. Our 3D structures for G1 and G2 will assist in understanding geometric formalism of G-quadruplex folding and may be helpful as a platform for rational anti-HIV drug design.

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

PubMed

de Ribaupierre, Sandrine; Wilson, Timothy D

2012-06-01

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

Ten Triangles around Cavernous Sinus for Surgical Approach, Described by Schematic Diagram and Three Dimensional Models with the Sectioned Images.

PubMed

Chung, Beom Sun; Ahn, Young Hwan; Park, Jin Seo

2016-09-01

For the surgical approach to lesions around the cavernous sinus (CS), triangular spaces around CS have been devised. However, educational materials for learning the triangles were insufficient. The purpose of this study is to present educational materials about the triangles, consisting of a schematic diagram and 3-dimensional (3D) models with sectioned images. To achieve the purposes, other studies were analyzed to establish new definitions and names of the triangular spaces. Learning materials including schematic diagrams and 3D models with cadaver's sectioned images were manufactured. Our new definition was attested by observing the sectioned images and 3D models. The triangles and the four representative surgical approaches were stereoscopically indicated on the 3D models. All materials of this study were put into Portable Document Format file and were distributed freely at our homepage (anatomy.dongguk.ac.kr/triangles). By using our schematic diagram and the 3D models with sectioned images, ten triangles and the related structures could be understood and observed accurately. We expect that our data will contribute to anatomy education, surgery training, and radiologic understanding of the triangles and related structures.

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

PubMed

Jain, Swati; Schlick, Tamar

2017-11-24

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

A New Calibration Method for Commercial RGB-D Sensors

PubMed Central

Darwish, Walid; Tang, Shenjun; Li, Wenbin; Chen, Wu

2017-01-01

Commercial RGB-D sensors such as Kinect and Structure Sensors have been widely used in the game industry, where geometric fidelity is not of utmost importance. For applications in which high quality 3D is required, i.e., 3D building models of centimeter-level accuracy, accurate and reliable calibrations of these sensors are required. This paper presents a new model for calibrating the depth measurements of RGB-D sensors based on the structured light concept. Additionally, a new automatic method is proposed for the calibration of all RGB-D parameters, including internal calibration parameters for all cameras, the baseline between the infrared and RGB cameras, and the depth error model. When compared with traditional calibration methods, this new model shows a significant improvement in depth precision for both near and far ranges. PMID:28538695

The evolution of void-filled cosmological structures

NASA Technical Reports Server (NTRS)

Regos, Eniko; Geller, Margaret J.

1991-01-01

1D, 2D, and 3D simulations are used here to investigate the salient features in the evolution of void-filled cosmological structures in universes with arbitrary values of Omega. It is found that the growth of a void as a function of time decreases significantly at the time corresponding to Omega = 0.5. In models constructed in 2D and 3D, suitable initial conditions lead to cellular structure with faceted voids similar to those observed in redshift surveys. Matter compressed to planes flows more rapidly toward condensations at the intersections than would be expected for spherical infall. The peculiar streaming velocities for void diameters of 5000 km/s should be observable. The simulations provide a more physical basis and dynamics for the bubbly and Voronois tesselation models used to derive statistical properties of cellular large-scale structure.

Dynamical mean-field theory on the real-frequency axis: p -d hybridization and atomic physics in SrMnO3

NASA Astrophysics Data System (ADS)

Bauernfeind, Daniel; Triebl, Robert; Zingl, Manuel; Aichhorn, Markus; Evertz, Hans Gerd

2018-03-01

We investigate the electronic structure of SrMnO3 with density functional theory plus dynamical mean-field theory (DMFT). Within this scheme the selection of the correlated subspace and the construction of the corresponding Wannier functions is a crucial step. Due to the crystal-field splitting of the Mn-3 d orbitals and their separation from the O -2 p bands, SrMnO3 is a material where on first sight a three-band d -only model should be sufficient. However, in the present work we demonstrate that the resulting spectrum is considerably influenced by the number of correlated orbitals and the number of bands included in the Wannier function construction. For example, in a d -d p model we observe a splitting of the t2 g lower Hubbard band into a more complex spectral structure, not observable in d -only models. To illustrate these high-frequency differences we employ the recently developed fork tensor product state (FTPS) impurity solver, as it provides the necessary spectral resolution on the real-frequency axis. We find that the spectral structure of a five-band d -d p model is in good agreement with PES and XAS experiments. Our results demonstrate that the FTPS solver is capable of performing full five-band DMFT calculations directly on the real-frequency axis.

Algorithms for extraction of structural attitudes from 3D outcrop models

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Full Three-Dimensional Tomography Experiments in the Western Pacific Region

NASA Astrophysics Data System (ADS)

Zhao, L.; Chen, L.; Jordan, T. H.

2001-12-01

Two decades of seismic tomography studies have yielded earth models with three-dimensional (3-D) velocity heterogeneities in the mantle on both global and regional scales. With the continuing improvements in inversion techniques, station coverage and computational facilities, seismic tomography has reached a stage at which higher resolution to the structure can only be achieved reliably by employing accurate descriptions between observables and structural parameters, especially in the upper mantle. With this in mind, we have conducted a tomography experiment for the mantle structure beneath the Western Pacific with a full 3-D approach: imaging the 3-D structure using true 3-D Fréchet kernels. In our experiment, we use nearly 20,000 delay times measured at eight discrete frequencies between 10mHz and 45mHz from three-component regional {S} waves, including its multiple reflections from the surface and the CMB. The 3-D Fréchet kernels for these delay times are computed by a normal-mode approach (Zhao, Jordan & Chapman 2000) in which coupling between each pair of modes is accounted for with the exception of cross coupling between spheroidal and toroidal modes. The algorithm is implemented with MPI on the 192-node (and expanding) dual-processor Linux-PC cluster at the University of Southern California. The 3-D radially anisotropic shear-speed model is obtained through a Gaussian-Bayesian inversion. A full description of features in our model will be given in a separate presentation (Chen, Zhao & Jordan, this meeting). Here we discuss in detail the issues related to the calculation of a large number of coupled-mode 3-D kernels for the frequency-dependent delay times and their inversion. We also examine the efficacy of this full 3-D approach in regional high-resolution tomography studies by comparing the results with those in our previous work in which the 3-D structure was obtained by inverting the same delay-time measurements but using computationally more efficient 2-D Fréchet kernels approximated from 3-D by an asymptotic stationary-phase integration across the great-circle plane.

Validation of Clay Modeling as a Learning Tool for the Periventricular Structures of the Human Brain

ERIC Educational Resources Information Center

Akle, Veronica; Peña-Silva, Ricardo A.; Valencia, Diego M.; Rincón-Perez, Carlos W.

2018-01-01

Visualizing anatomical structures and functional processes in three dimensions (3D) are important skills for medical students. However, contemplating 3D structures mentally and interpreting biomedical images can be challenging. This study examines the impact of a new pedagogical approach to teaching neuroanatomy, specifically how building a…

Generating Accurate 3d Models of Architectural Heritage Structures Using Low-Cost Camera and Open Source Algorithms

NASA Astrophysics Data System (ADS)

Zacharek, M.; Delis, P.; Kedzierski, M.; Fryskowska, A.

2017-05-01

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

NMR Model of PrgI-SipD Interaction and its Implications in the Needle-Tip Assembly of the Salmonella Type III Secretion System

PubMed Central

Rathinavelan, Thenmalarchelvi; Lara-Tejero, Maria; Lefebre, Matthew; Chatterjee, Srirupa; McShan, Andrew C.; Guo, Da-Chuan; Tang, Chun; Galan, Jorge E.; De Guzman, Roberto N.

2014-01-01

Salmonella and other pathogenic bacteria use the type III secretion system (T3SS) to inject virulence proteins into human cells to initiate infections. The structural component of the T3SS contains a needle and a needle tip. The needle is assembled from PrgI needle protomers and the needle tip is capped with several copies of the SipD tip protein. How a tip protein docks on the needle is unclear. A crystal structure of a PrgI-SipD fusion protein docked on the PrgI needle results in steric clash of SipD at the needle tip when modeled on the recent atomic structure of the needle. Thus, there is currently no good model of how SipD is docked on the PrgI needle tip. Previously, we showed by NMR paramagnetic relaxation enhancement (PRE) methods that a specific region in the SipD coiled-coil is the binding site for PrgI. Others have hypothesized that a domain of the tip protein – the N-terminal α-helical hairpin, has to swing away during the assembly of the needle apparatus. Here, we show by PRE methods that a truncated form of SipD lacking the α-helical hairpin domain binds more tightly to PrgI. Further, PRE-based structure calculations revealed multiple PrgI binding sites on the SipD coiled-coil. Our PRE results together with the recent NMR-derived atomic structure of the Salmonella needle suggest a possible model of how SipD might dock at the PrgI needle tip. SipD and PrgI are conserved in other bacterial T3SSs, thus our results have wider implication in understanding other needle-tip complexes. PMID:24951833

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

NASA Astrophysics Data System (ADS)

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

2008-12-01

We determine finite fault models of the 2004 Parkfield earthquake using 3D Green's functions. Because of the dense station coverage and detailed 3D velocity structure model in this region, this earthquake provides an excellent opportunity to examine how the 3D velocity structure affects the finite fault inverse solutions. Various studies (e.g. Michaels and Eberhart-Phillips, 1991; Thurber et al., 2006) indicate that there is a pronounced velocity contrast across the San Andreas Fault along the Parkfield segment. Also the fault zone at Parkfield is wide as evidenced by mapped surface faults and where surface slip and creep occurred in the 1966 and the 2004 Parkfield earthquakes. For high resolution images of the rupture process"Ait is necessary to include the accurate 3D velocity structure for the finite source inversion. Liu and Aurchuleta (2004) performed finite fault inversions using both 1D and 3D Green's functions for 1989 Loma Prieta earthquake using the same source paramerization and data but different Green's functions and found that the models were quite different. This indicates that the choice of the velocity model significantly affects the waveform modeling at near-fault stations. In this study, we used the P-wave velocity model developed by Thurber et al (2006) to construct the 3D Green's functions. P-wave speeds are converted to S-wave speeds and density using by the empirical relationships of Brocher (2005). Using a finite difference method, E3D (Larsen and Schultz, 1995), we computed the 3D Green's functions numerically by inserting body forces at each station. Using reciprocity, these Green's functions are recombined to represent the ground motion at each station due to the slip on the fault plane. First we modeled the waveforms of small earthquakes to validate the 3D velocity model and the reciprocity of the Green"fs function. In the numerical tests we found that the 3D velocity model predicted the individual phases well at frequencies lower than 0.25 Hz but that the velocity model is fast at stations located very close to the fault. In this near-fault zone the model also underpredicts the amplitudes. This implies the need to include an additional low velocity zone in the fault zone to fit the data. For the finite fault modeling we use the same stations as in our previous study (Kim and Dreger 2008), and compare the results to investigate the effect of 3D Green's functions on kinematic source inversions. References: Brocher, T. M., (2005), Empirical relations between elastic wavespeeds and density in the Earth's crust, Bull. Seism. Soc. Am., 95, No. 6, 2081-2092. Eberhart-Phillips, D., and A.J. Michael, (1993), Three-dimensional velocity structure and seismicity in the Parkfield region, central California, J. Geophys. Res., 98, 15,737-15,758. Kim A., D. S. Dreger (2008), Rupture process of the 2004 Parkfield earthquake from near-fault seismic waveform and geodetic records, J. Geophys. Res., 113, B07308. Thurber, C., H. Zhang, F. Waldhauser, J. Hardebeck, A. Michaels, and D. Eberhart-Phillips (2006), Three- dimensional compressional wavespeed model, earthquake relocations, and focal mechanisms for the Parkfield, California, region, Bull. Seism. Soc. Am., 96, S38-S49. Larsen, S., and C. A. Schultz (1995), ELAS3D: 2D/3D elastic finite-difference wave propagation code, Technical Report No. UCRL-MA-121792, 19pp. Liu, P., and R. J. Archuleta (2004), A new nonlinear finite fault inversion with three-dimensional Green's functions: Application to the 1989 Loma Prieta, California, earthquake, J. Geophys. Res., 109, B02318.

Structural models for the design of novel antiviral agents against Greek Goat Encephalitis

PubMed Central

Papageorgiou, Louis; Loukatou, Styliani; Koumandou, Vassiliki Lila; Makałowski, Wojciech; Megalooikonomou, Vasileios

2014-01-01

The Greek Goat Encephalitis virus (GGE) belongs to the Flaviviridae family of the genus Flavivirus. The GGE virus constitutes an important pathogen of livestock that infects the goat’s central nervous system. The viral enzymes of GGE, helicase and RNA-dependent RNA polymerase (RdRP), are ideal targets for inhibitor design, since those enzymes are crucial for the virus’ survival, proliferation and transmission. In an effort to understand the molecular structure underlying the functions of those viral enzymes, the three dimensional structures of GGE NS3 helicase and NS5 RdRP have been modelled. The models were constructed in silico using conventional homology modelling techniques and the known 3D crystal structures of solved proteins from closely related species as templates. The established structural models of the GGE NS3 helicase and NS5 RdRP have been evaluated for their viability using a repertoire of in silico tools. The goal of this study is to present the 3D conformations of the GGE viral enzymes as reliable structural models that could provide the platform for the design of novel anti-GGE agents. PMID:25392762

Parametric modelling design applied to weft knitted surfaces and its effects in their physical properties

NASA Astrophysics Data System (ADS)

Oliveira, N. P.; Maciel, L.; Catarino, A. P.; Rocha, A. M.

2017-10-01

This work proposes the creation of models of surfaces using a parametric computer modelling software to obtain three-dimensional structures in weft knitted fabrics produced on single needle system machines. Digital prototyping, another feature of digital modelling software, was also explored in three-dimensional drawings generated using the Rhinoceros software. With this approach, different 3D structures were developed and produced. Physical characterization tests were then performed on the resulting 3D weft knitted structures to assess their ability to promote comfort. From the obtained results, it is apparent that the developed structures have potential for application in different market segments, such as clothing and interior textiles.

Feasibility of rapid and automated importation of 3D echocardiographic left ventricular (LV) geometry into a finite element (FEM) analysis model

PubMed Central

Verhey, Janko F; Nathan, Nadia S

2004-01-01

Background Finite element method (FEM) analysis for intraoperative modeling of the left ventricle (LV) is presently not possible. Since 3D structural data of the LV is now obtainable using standard transesophageal echocardiography (TEE) devices intraoperatively, the present study describes a method to transfer this data into a commercially available FEM analysis system: ABAQUS©. Methods In this prospective study TomTec LV Analysis TEE© Software was used for semi-automatic endocardial border detection, reconstruction, and volume-rendering of the clinical 3D echocardiographic data. A newly developed software program MVCP FemCoGen©, written in Delphi, reformats the TomTec file structures in five patients for use in ABAQUS and allows visualization of regional deformation of the LV. Results This study demonstrates that a fully automated importation of 3D TEE data into FEM modeling is feasible and can be efficiently accomplished in the operating room. Conclusion For complete intraoperative 3D LV finite element analysis, three input elements are necessary: 1. time-gaited, reality-based structural information, 2. continuous LV pressure and 3. instantaneous tissue elastance. The first of these elements is now available using the methods presented herein. PMID:15473901

Geophysical Modeling in Eurasia: 2D Crustal P and LG Propagation; Upper- Mantle Shear Wave Propagation and Anisotropy; and 3D, Joint, Simultaneous Inversions

DTIC Science & Technology

2008-09-01

improved resolution for shallow geologic structures . Jointly inverting these datasets with seismic body wave (S) travel times provides additional...constraints on the shallow structure and an enhanced 3D shear wave model for our study area in western China. 2008 Monitoring Research Review...for much of Eurasia, although the Arabian Shield and Arctic are less well recovered. The upper velocity gradient was tested for 10-degree cells

Stochastic and Geometric Reasoning for Indoor Building Models with Electric Installations - Bridging the Gap Between GIS and Bim

NASA Astrophysics Data System (ADS)

Dehbi, Y.; Haunert, J.-H.; Plümer, L.

2017-10-01

3D city and building models according to CityGML encode the geometry, represent the structure and model semantically relevant building parts such as doors, windows and balconies. Building information models support the building design, construction and the facility management. In contrast to CityGML, they include also objects which cannot be observed from the outside. The three dimensional indoor models characterize a missing link between both worlds. Their derivation, however, is expensive. The semantic automatic interpretation of 3D point clouds of indoor environments is a methodically demanding task. The data acquisition is costly and difficult. The laser scanners and image-based methods require the access to every room. Based on an approach which does not require an additional geometry acquisition of building indoors, we propose an attempt for filling the gaps between 3D building models and building information models. Based on sparse observations such as the building footprint and room areas, 3D indoor models are generated using combinatorial and stochastic reasoning. The derived models are expanded by a-priori not observable structures such as electric installation. Gaussian mixtures, linear and bi-linear constraints are used to represent the background knowledge and structural regularities. The derivation of hypothesised models is performed by stochastic reasoning using graphical models, Gauss-Markov models and MAP-estimators.

A 3D Bioprinted Model for the Study of Premalignant Breast Disease

DTIC Science & Technology

2017-05-01

these glands and performed proof-of-principle 3D printing . We have printed simple ductal structures (tubes) and seeded breast epithelial cells. The...performed proof-of-principle 3D printing . We have printed simple ductal structures (tubes) and seeded breast epithelial cells. The next year we will...All of the PN17 reconstruction data from the 5 completed strains has also been sent to the University of Pittsburg for 3D printing . A summary of the

The NIH 3D Print Exchange: A Public Resource for Bioscientific and Biomedical 3D Prints.

PubMed

Coakley, Meghan F; Hurt, Darrell E; Weber, Nick; Mtingwa, Makazi; Fincher, Erin C; Alekseyev, Vsevelod; Chen, David T; Yun, Alvin; Gizaw, Metasebia; Swan, Jeremy; Yoo, Terry S; Huyen, Yentram

2014-09-01

The National Institutes of Health (NIH) has launched the NIH 3D Print Exchange, an online portal for discovering and creating bioscientifically relevant 3D models suitable for 3D printing, to provide both researchers and educators with a trusted source to discover accurate and informative models. There are a number of online resources for 3D prints, but there is a paucity of scientific models, and the expertise required to generate and validate such models remains a barrier. The NIH 3D Print Exchange fills this gap by providing novel, web-based tools that empower users with the ability to create ready-to-print 3D files from molecular structure data, microscopy image stacks, and computed tomography scan data. The NIH 3D Print Exchange facilitates open data sharing in a community-driven environment, and also includes various interactive features, as well as information and tutorials on 3D modeling software. As the first government-sponsored website dedicated to 3D printing, the NIH 3D Print Exchange is an important step forward to bringing 3D printing to the mainstream for scientific research and education.

Absolute earthquake locations using 3-D versus 1-D velocity models below a local seismic network: example from the Pyrenees

NASA Astrophysics Data System (ADS)

Theunissen, T.; Chevrot, S.; Sylvander, M.; Monteiller, V.; Calvet, M.; Villaseñor, A.; Benahmed, S.; Pauchet, H.; Grimaud, F.

2018-03-01

Local seismic networks are usually designed so that earthquakes are located inside them (primary azimuthal gap <<180°) and close to the seismic stations (0-100 km). With these local or near-regional networks (0°-5°), many seismological observatories still routinely locate earthquakes using 1-D velocity models. Moving towards 3-D location algorithms requires robust 3-D velocity models. This work takes advantage of seismic monitoring spanning more than 30 yr in the Pyrenean region. We investigate the influence of a well-designed 3-D model with station corrections including basins structure and the geometry of the Mohorovicic discontinuity on earthquake locations. In the most favourable cases (GAP < 180° and distance to the first station lower than 15 km), results using 1-D velocity models are very similar to 3-D results. The horizontal accuracy in the 1-D case can be higher than in the 3-D case if lateral variations in the structure are not properly resolved. Depth is systematically better resolved in the 3-D model even on the boundaries of the seismic network (GAP > 180° and distance to the first station higher than 15 km). Errors on velocity models and accuracy of absolute earthquake locations are assessed based on a reference data set made of active seismic, quarry blasts and passive temporary experiments. Solutions and uncertainties are estimated using the probabilistic approach of the NonLinLoc (NLLoc) software based on Equal Differential Time. Some updates have been added to NLLoc to better focus on the final solution (outlier exclusion, multiscale grid search, S-phases weighting). Errors in the probabilistic approach are defined to take into account errors on velocity models and on arrival times. The seismicity in the final 3-D catalogue is located with a horizontal uncertainty of about 2.0 ± 1.9 km and a vertical uncertainty of about 3.0 ± 2.0 km.

Capillary Origami Inspired Fabrication of Complex 3D Hydrogel Constructs.

PubMed

Li, Moxiao; Yang, Qingzhen; Liu, Hao; Qiu, Mushu; Lu, Tian Jian; Xu, Feng

2016-09-01

Hydrogels have found broad applications in various engineering and biomedical fields, where the shape and size of hydrogels can profoundly influence their functions. Although numerous methods have been developed to tailor 3D hydrogel structures, it is still challenging to fabricate complex 3D hydrogel constructs. Inspired by the capillary origami phenomenon where surface tension of a droplet on an elastic membrane can induce spontaneous folding of the membrane into 3D structures along with droplet evaporation, a facile strategy is established for the fabrication of complex 3D hydrogel constructs with programmable shapes and sizes by crosslinking hydrogels during the folding process. A mathematical model is further proposed to predict the temporal structure evolution of the folded 3D hydrogel constructs. Using this model, precise control is achieved over the 3D shapes (e.g., pyramid, pentahedron, and cube) and sizes (ranging from hundreds of micrometers to millimeters) through tuning membrane shape, dimensionless parameter of the process (elastocapillary number Ce ), and evaporation time. This work would be favorable to multiple areas, such as flexible electronics, tissue regeneration, and drug delivery. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation Studies of the Effect of Forest Spatial Structure on InSAR Signature

NASA Technical Reports Server (NTRS)

Sun, Guoqing; Liu, Dawei; Ranson, K. Jon; Koetz, Benjamin

2007-01-01

The height of scattering phase retrieved from InSAR data is considered being correlated with the tree height and the spatial structure of the forest stand. Though some researchers have used simple backscattering models to estimate tree height from the height of scattering center, the effect of forest spatial structure on InSAR data is not well understood yet. A three-dimensional coherent radar backscattering model for forest canopies based on realistic three-dimensional scene was used to investigate the effect in this paper. The realistic spatial structure of forest canopies was established either by field measurements (stem map) or through use of forest growth model. Field measurements or a forest growth model parameterized using local environmental parameters provides information of forest species composition and tree sizes in certain growth phases. A fractal tree model (L-system) was used to simulate individual 3- D tree structure of different ages or heights. Trees were positioned in a stand in certain patterns resulting in a 3-D medium of discrete scatterers. The radar coherent backscatter model took the 3-D forest scene as input and simulates the coherent radar backscattering signature. Interferometric SAR images of 3D scenes were simulated and heights of scattering phase centers were estimated from the simulated InSAR data. The effects of tree height, crown cover, crown depth, and the spatial distribution patterns of trees on the scattering phase center were analyzed. The results will be presented in the paper.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

To What Degree Does Handling Concrete Molecular Models Promote the Ability to Translate and Coordinate between 2D and 3D Molecular Structure Representations? A Case Study with Algerian Students

ERIC Educational Resources Information Center

Mohamed-Salah, Boukhechem; Alain, Dumon

2016-01-01

This study aims to assess whether the handling of concrete ball-and-stick molecular models promotes translation between diagrammatic representations and a concrete model (or vice versa) and the coordination of the different types of structural representations of a given molecular structure. Forty-one Algerian undergraduate students were requested…

Emerging Applications of Bedside 3D Printing in Plastic Surgery

PubMed Central

Chae, Michael P.; Rozen, Warren M.; McMenamin, Paul G.; Findlay, Michael W.; Spychal, Robert T.; Hunter-Smith, David J.

2015-01-01

Modern imaging techniques are an essential component of preoperative planning in plastic and reconstructive surgery. However, conventional modalities, including three-dimensional (3D) reconstructions, are limited by their representation on 2D workstations. 3D printing, also known as rapid prototyping or additive manufacturing, was once the province of industry to fabricate models from a computer-aided design (CAD) in a layer-by-layer manner. The early adopters in clinical practice have embraced the medical imaging-guided 3D-printed biomodels for their ability to provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. With increasing accessibility, investigators are able to convert standard imaging data into a CAD file using various 3D reconstruction softwares and ultimately fabricate 3D models using 3D printing techniques, such as stereolithography, multijet modeling, selective laser sintering, binder jet technique, and fused deposition modeling. However, many clinicians have questioned whether the cost-to-benefit ratio justifies its ongoing use. The cost and size of 3D printers have rapidly decreased over the past decade in parallel with the expiration of key 3D printing patents. Significant improvements in clinical imaging and user-friendly 3D software have permitted computer-aided 3D modeling of anatomical structures and implants without outsourcing in many cases. These developments offer immense potential for the application of 3D printing at the bedside for a variety of clinical applications. In this review, existing uses of 3D printing in plastic surgery practice spanning the spectrum from templates for facial transplantation surgery through to the formation of bespoke craniofacial implants to optimize post-operative esthetics are described. Furthermore, we discuss the potential of 3D printing to become an essential office-based tool in plastic surgery to assist in preoperative planning, developing intraoperative guidance tools, teaching patients and surgical trainees, and producing patient-specific prosthetics in everyday surgical practice. PMID:26137465

Emerging Applications of Bedside 3D Printing in Plastic Surgery.

PubMed

Chae, Michael P; Rozen, Warren M; McMenamin, Paul G; Findlay, Michael W; Spychal, Robert T; Hunter-Smith, David J

2015-01-01

Modern imaging techniques are an essential component of preoperative planning in plastic and reconstructive surgery. However, conventional modalities, including three-dimensional (3D) reconstructions, are limited by their representation on 2D workstations. 3D printing, also known as rapid prototyping or additive manufacturing, was once the province of industry to fabricate models from a computer-aided design (CAD) in a layer-by-layer manner. The early adopters in clinical practice have embraced the medical imaging-guided 3D-printed biomodels for their ability to provide tactile feedback and a superior appreciation of visuospatial relationship between anatomical structures. With increasing accessibility, investigators are able to convert standard imaging data into a CAD file using various 3D reconstruction softwares and ultimately fabricate 3D models using 3D printing techniques, such as stereolithography, multijet modeling, selective laser sintering, binder jet technique, and fused deposition modeling. However, many clinicians have questioned whether the cost-to-benefit ratio justifies its ongoing use. The cost and size of 3D printers have rapidly decreased over the past decade in parallel with the expiration of key 3D printing patents. Significant improvements in clinical imaging and user-friendly 3D software have permitted computer-aided 3D modeling of anatomical structures and implants without outsourcing in many cases. These developments offer immense potential for the application of 3D printing at the bedside for a variety of clinical applications. In this review, existing uses of 3D printing in plastic surgery practice spanning the spectrum from templates for facial transplantation surgery through to the formation of bespoke craniofacial implants to optimize post-operative esthetics are described. Furthermore, we discuss the potential of 3D printing to become an essential office-based tool in plastic surgery to assist in preoperative planning, developing intraoperative guidance tools, teaching patients and surgical trainees, and producing patient-specific prosthetics in everyday surgical practice.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

3D Nanoporous Anodic Alumina Structures for Sustained Drug Release

PubMed Central

Xifré-Pérez, Elisabet; Eckstein, Chris; Ferré-Borrull, Josep

2017-01-01

The use of nanoporous anodic alumina (NAA) for the development of drug delivery systems has gained much attention in recent years. The release of drugs loaded inside NAA pores is complex and depends on the morphology of the pores. In this study, NAA, with different three-dimensional (3D) pore structures (cylindrical pores with several pore diameters, multilayered nanofunnels, and multilayered inverted funnels) were fabricated, and their respective drug delivery rates were studied and modeled using doxorubicin as a model drug. The obtained results reveal optimal modeling of all 3D pore structures, differentiating two drug release stages. Thus, an initial short-term and a sustained long-term release were successfully modeled by the Higuchi and the Korsmeyer–Peppas equations, respectively. This study demonstrates the influence of pore geometries on drug release rates, and further presents a sustained long-term drug release that exceeds 60 days without an undesired initial burst. PMID:28825654

3D Documentation and BIM Modeling of Cultural Heritage Structures Using UAVs: The Case of the Foinikaria Church

NASA Astrophysics Data System (ADS)

Themistocleous, K.; Agapiou, A.; Hadjimitsis, D.

2016-10-01

The documentation of architectural cultural heritage sites has traditionally been expensive and labor-intensive. New innovative technologies, such as Unmanned Aerial Vehicles (UAVs), provide an affordable, reliable and straightforward method of capturing cultural heritage sites, thereby providing a more efficient and sustainable approach to documentation of cultural heritage structures. In this study, hundreds of images of the Panagia Chryseleousa church in Foinikaria, Cyprus were taken using a UAV with an attached high resolution camera. The images were processed to generate an accurate digital 3D model by using Structure in Motion techniques. Building Information Model (BIM) was then used to generate drawings of the church. The methodology described in the paper provides an accurate, simple and cost-effective method of documenting cultural heritage sites and generating digital 3D models using novel techniques and innovative methods.

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

NASA Technical Reports Server (NTRS)

Belknap, Shannon; Zhang, Michael

2013-01-01

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

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 problem for the inversion of dispersion curves.

Re-refinement of the spliceosomal U4 snRNP core-domain structure

PubMed Central

Li, Jade; Leung, Adelaine K.; Kondo, Yasushi; Oubridge, Chris; Nagai, Kiyoshi

2016-01-01

The core domain of small nuclear ribonucleoprotein (snRNP), comprised of a ring of seven paralogous proteins bound around a single-stranded RNA sequence, functions as the assembly nucleus in the maturation of U1, U2, U4 and U5 spliceosomal snRNPs. The structure of the human U4 snRNP core domain was initially solved at 3.6 Å resolution by experimental phasing using data with tetartohedral twinning. Molecular replacement from this model followed by density modification using untwinned data recently led to a structure of the minimal U1 snRNP at 3.3 Å resolution. With the latter structure providing a search model for molecular replacement, the U4 core-domain structure has now been re-refined. The U4 Sm site-sequence AAUUUUU has been shown to bind to the seven Sm proteins SmF–SmE–SmG–SmD3–SmB–SmD1–SmD2 in an identical manner as the U1 Sm-site sequence AAUUUGU, except in SmD1 where the bound U replaces G. The progression from the initial to the re-refined structure exemplifies a tortuous route to accuracy: where well diffracting crystals of complex assemblies are initially unavailable, the early model errors are rectified by exploiting preliminary interpretations in further experiments involving homologous structures. New insights are obtained from the more accurate model. PMID:26894541

The seismic response of the Los Angeles basin, California

USGS Publications Warehouse

Wald, D.J.; Graves, R.W.

1998-01-01

Using strong-motion data recorded in the Los Angeles region from the 1992 (Mw 7.3) Landers earthquake, we have tested the accuracy of existing three-dimensional (3D) velocity models on the simulation of long-period (???2 sec) ground motions in the Los Angeles basin and surrounding San Fernando and San Gabriel Valleys. First, the overall pattern and degree of long-period excitation of the basins were identified in the observations. Within the Los Angeles basin, the recorded amplitudes are about three to four times larger than at sites outside the basins; amplitudes within the San Fernando and San Gabriel Valleys are nearly a factor of 3 greater than surrounding bedrock sites. Then, using a 3D finite-difference numerical modeling approach, we analyzed how variations in 3D earth structure affect simulated waveforms, amplitudes, and the fit to the observed patterns of amplification. Significant differences exist in the 3D velocity models of southern California that we tested (Magistrale et al., 1996; Graves, 1996a; Hauksson and Haase, 1997). Major differences in the models include the velocity of the assumed background models; the depth of the Los Angeles basin; and the depth, location, and geometry of smaller basins. The largest disparities in the response of the models are seen for the San Fernando Valley and the deepest portion of the Los Angeles basin. These arise in large part from variations in the structure of the basins, particularly the effective depth extent, which is mainly due to alternative assumptions about the nature of the basin sediment fill. The general ground-motion characteristics are matched by the 3D model simulations, validating the use of 3D modeling with geologically based velocity-structure models. However, significant shortcomings exist in the overall patterns of amplification and the duration of the long-period response. The successes and limitations of the models for reproducing the recorded ground motions as discussed provide the basis and direction for necessary improvements to earth structure models, whether geologically or tomographically derived. The differences in the response of the earth models tested also translate to variable success in the ability to successfully model the data and add uncertainty to estimates of the basin response given input "scenario" earthquake source models.

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

NASA Langley developments in response calculations needed for failure and life prediction

NASA Technical Reports Server (NTRS)

Housner, Jerrold M.

1993-01-01

NASA Langley developments in response calculations needed for failure and life predictions are discussed. Topics covered include: structural failure analysis in concurrent engineering; accuracy of independent regional modeling demonstrated on classical example; functional interface method accurately joins incompatible finite element models; interface method for insertion of local detail modeling extended to curve pressurized fuselage window panel; interface concept for joining structural regions; motivation for coupled 2D-3D analysis; compression panel with discontinuous stiffener coupled 2D-3D model and axial surface strains at the middle of the hat stiffener; use of adaptive refinement with multiple methods; adaptive mesh refinement; and studies on quantity effect of bow-type initial imperfections on reliability of stiffened panels.

3D model retrieval method based on mesh segmentation

NASA Astrophysics Data System (ADS)

Gan, Yuanchao; Tang, Yan; Zhang, Qingchen

2012-04-01

In the process of feature description and extraction, current 3D model retrieval algorithms focus on the global features of 3D models but ignore the combination of global and local features of the model. For this reason, they show less effective performance to the models with similar global shape and different local shape. This paper proposes a novel algorithm for 3D model retrieval based on mesh segmentation. The key idea is to exact the structure feature and the local shape feature of 3D models, and then to compares the similarities of the two characteristics and the total similarity between the models. A system that realizes this approach was built and tested on a database of 200 objects and achieves expected results. The results show that the proposed algorithm improves the precision and the recall rate effectively.

3D structure of the influenza virus polymerase complex: Localization of subunit domains

PubMed Central

Area, Estela; Martín-Benito, Jaime; Gastaminza, Pablo; Torreira, Eva; Valpuesta, José M.; Carrascosa, José L.; Ortín, Juan

2004-01-01

The 3D structure of the influenza virus polymerase complex was determined by electron microscopy and image processing of recombinant ribonucleoproteins (RNPs). The RNPs were generated by in vivo amplification using cDNAs of the three polymerase subunits, the nucleoprotein, and a model virus-associated RNA containing 248 nt. The polymerase structure obtained is very compact, with no apparent boundaries among subunits. The position of specific regions of the PB1, PB2, and PA subunits was determined by 3D reconstruction of either RNP–mAb complexes or tagged RNPs. This structural model is available for the polymerase of a negative-stranded RNA virus and provides a general delineation of the complex and its interaction with the template-associated nucleoprotein monomers in the RNP. PMID:14691253

Electronic structure and magnetic anisotropy of L1{sub 0}-FePt thin film studied by hard x-ray photoemission spectroscopy and first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ueda, S.; Synchrotron X-ray Station at SPring-8, National Institute for Materials Science, Sayo, Hyogo 679-5148; Mizuguchi, M.

2016-07-25

We have studied the electronic structure of the L1{sub 0} ordered FePt thin film by hard x-ray photoemission spectroscopy (HAXPES), cluster model, and first-principles calculations to investigate the relationship between the electronic structure and perpendicular magneto-crystalline anisotropy (MCA). The Fe 2p core-level HAXPES spectrum of the ordered film revealed the strong electron correlation in the Fe 3d states and the hybridization between the Fe 3d and Pt 5d states. By comparing the experimental valence band structure with the theoretical density of states, the strong electron correlation in the Fe 3d states modifies the valence band electronic structure of the L1{submore » 0} ordered FePt thin film through the Fe 3d-Pt 5d hybridization. These results strongly suggest that the strong electron correlation effect in the Fe 3d states and the Fe 3d-Pt 5d hybridization as well as the spin-orbit interaction in the Pt 5d states play important roles in the perpendicular MCA for L1{sub 0}-FePt.« less

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

PubMed

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

2013-09-01

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

Space-time evolution of a growth fold (Betic Cordillera, Spain). Evidences from 3D geometrical modelling

NASA Astrophysics Data System (ADS)

Martin-Rojas, Ivan; Alfaro, Pedro; Estévez, Antonio

2014-05-01

We present a study that encompasses several software tools (iGIS©, ArcGIS©, Autocad©, etc.) and data (geological mapping, high resolution digital topographic data, high resolution aerial photographs, etc.) to create a detailed 3D geometric model of an active fault propagation growth fold. This 3D model clearly shows structural features of the analysed fold, as well as growth relationships and sedimentary patterns. The results obtained permit us to discuss the kinematics and structural evolution of the fold and the fault in time and space. The study fault propagation fold is the Crevillente syncline. This fold represents the northern limit of the Bajo Segura Basin, an intermontane basin in the Eastern Betic Cordillera (SE Spain) developed from upper Miocene on. 3D features of the Crevillente syncline, including growth pattern, indicate that limb rotation and, consequently, fault activity was higher during Messinian than during Tortonian; consequently, fault activity was also higher. From Pliocene on our data point that limb rotation and fault activity steadies or probably decreases. This in time evolution of the Crevillente syncline is not the same all along the structure; actually the 3D geometric model indicates that observed lateral heterogeneity is related to along strike variation of fault displacement.

Three-dimensional joint inversion for magnetotelluric resistivity and static shift distributions in complex media

NASA Astrophysics Data System (ADS)

Sasaki, Yutaka; Meju, Max A.

2006-05-01

Accurate interpretation of magnetotelluric (MT) data in the presence of static shift arising from near-surface inhomogeneities is an unresolved problem in three-dimensional (3-D) inversion. While it is well known in 1-D and 2-D studies that static shift can lead to erroneous interpretation, how static shift can influence the result of 3-D inversion is not fully understood and is relevant to improved subsurface analysis. Using the synthetic data generated from 3-D models with randomly distributed heterogeneous overburden and elongate homogeneous overburden that are consistent with geological observations, this paper examines the effects of near-surface inhomogeneity on the accuracy of 3-D inversion models. It is found that small-scale and shallow depth structures are severely distorted while the large-scale structure is marginally distorted in 3-D inversion not accounting for static shift; thus the erroneous near-surface structure does degrade the reconstruction of smaller-scale structure at any depth. However, 3-D joint inversion for resistivity and static shift significantly reduces the artifacts caused by static shifts and improves the overall resolution, irrespective of whether a zero-sum or Gaussian distribution of static shifts is assumed. The 3-D joint inversion approach works equally well for situations where the shallow bodies are of small size or long enough to allow some induction such that the effects of near-surface inhomogeneity are manifested as a frequency-dependent shift rather than a constant shift.

Research on complex 3D tree modeling based on L-system

NASA Astrophysics Data System (ADS)

Gang, Chen; Bin, Chen; Yuming, Liu; Hui, Li

2018-03-01

L-system as a fractal iterative system could simulate complex geometric patterns. Based on the field observation data of trees and knowledge of forestry experts, this paper extracted modeling constraint rules and obtained an L-system rules set. Using the self-developed L-system modeling software the L-system rule set was parsed to generate complex tree 3d models.The results showed that the geometrical modeling method based on l-system could be used to describe the morphological structure of complex trees and generate 3D tree models.

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

PubMed

Barak, Meir Max; Black, Margaret Arielle

2018-02-01

Trabecular bone structure is crucial to normal mechanical behavior of bones. Studies have shown that osteoporosis negatively affects trabecular bone structure, mainly by reducing bone volume fraction (BV/TV) and thus increasing fracture risk. One major limitation in assessing and quantifying the effect of this structural deterioration is that no two trabecular structures are identical. Thus, when we compare a group of healthy bones against a different group of bones that experienced resorption (i.e. decreased BV/TV) we only discover an "average" mechanical effect. It is impossible to quantify the mechanical effect of individual structural deterioration for each sample, simply because we never have the same sample in both states (intact and deteriorated structure). 3D printing is a new technology that can assist in overcoming this issue. Here we report a preliminary study that compares a healthy 3D printed trabecular bone model with the same model after bone resorption was simulated. Since the deteriorated structural bone model is derived from the healthy one, it is possible to directly estimate (percentage wise) the decrease of tissue stiffness and strength as a result of bone resorption for this specific structure. Our results demonstrate that a relatively small decrease in BV/TV (about 8%) leads to a dramatic decrease in structural strength (24%) and structural stiffness (17%), (P < 0.01). Structural strength decreased from an average of 9.14 ± 2.85MPa to 6.97 ± 2.44MPa, while structural stiffness decreased from an average of 282.5 ± 63.4N/mm to 233.8 ± 51.2N/mm. This study demonstrates that 3D printing is a novel and valuable tool for quantifying the effect of structural deterioration on the mechanical properties of trabecular bone. In the future, this approach may help us attain better personal fracture risk assessments by CT scanning, 3D printing and mechanically testing individual bone replicas from patients suffering excessive bone resorption. Copyright © 2017 Elsevier Ltd. All rights reserved.

Receptor-based 3D-QSAR in Drug Design: Methods and Applications in Kinase Studies.

PubMed

Fang, Cheng; Xiao, Zhiyan

2016-01-01

Receptor-based 3D-QSAR strategy represents a superior integration of structure-based drug design (SBDD) and three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. It combines the accurate prediction of ligand poses by the SBDD approach with the good predictability and interpretability of statistical models derived from the 3D-QSAR approach. Extensive efforts have been devoted to the development of receptor-based 3D-QSAR methods and two alternative approaches have been exploited. One associates with computing the binding interactions between a receptor and a ligand to generate structure-based descriptors for QSAR analyses. The other concerns the application of various docking protocols to generate optimal ligand poses so as to provide reliable molecular alignments for the conventional 3D-QSAR operations. This review highlights new concepts and methodologies recently developed in the field of receptorbased 3D-QSAR, and in particular, covers its application in kinase studies.

3D Density Structure of Oceanic Lithosphere Affected by A Plume: A Case Study from the Greater Jan Mayen-East Greenland Region (NE Atlantic)

NASA Astrophysics Data System (ADS)

Tan, P.; Sippel, J.; Breivik, A. J.; Scheck-Wenderoth, M.; Meeßen, C.

2017-12-01

Unraveling the density structure of the oceanic lithosphere north of Iceland is key for understanding the effects of the Iceland Plume on the mid-ocean ridges of the greater Jan Mayen-East Greenland Region. We use a data-integrative approach for 3D gravity modeling to develop new insights into the crust and upper mantle density structure of this region. First, we obtain the 3D density structure of the sediments and crust from interpretations of regional reflection and refraction seismic lines. Then, the temperature and density structure of the mantle between 50 and 250 km are derived from a published shear-wave velocity (Vs) tomography model. To assess the density configuration between the Moho and 50 km depth, we follow a combined forward and inverse 3D gravity modeling approach. The Vs tomography and derived density of the deeper mantle (>50 km depth) reveal that the low-density anomaly related to the Iceland plume gets weaker with increasing distance from the plume, i.e. from the strongly influenced Middle Kolbeinsey Ridge (MKR) to the Mohn's Ridge. The West Jan Mayen Fracture Zone is identified as a main mantle density contrast, indicative of differences in the thermal evolution of the ridge systems it separates. Beneath the MKR region, the low-density anomaly at depths of >50 km continues upwards into the uppermost mantle, where its lateral dimensions narrow considerably. This elongated density anomaly is consistent with a basement high and indicates a channelization of the Iceland plume effects. The NE-SW elongated mantle anomaly does not, however, coincide with the topographical NNE-SSW striking ridge axis. Thus, the modelled plume-affected oceanic lithosphere reveals discrepancies with the half-space cooling model. We discuss the 3D density model in terms of such spatial relations between deeper mantle anomalies and the shallow crustal structure.

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

NASA Astrophysics Data System (ADS)

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

2006-02-01

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

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

ERIC Educational Resources Information Center

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2010-01-01

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

Enhancing Close-Up Image Based 3d Digitisation with Focus Stacking

NASA Astrophysics Data System (ADS)

Kontogianni, G.; Chliverou, R.; Koutsoudis, A.; Pavlidis, G.; Georgopoulos, A.

2017-08-01

The 3D digitisation of small artefacts is a very complicated procedure because of their complex morphological feature structures, concavities, rich decorations, high frequency of colour changes in texture, increased accuracy requirements etc. Image-based methods present a low cost, fast and effective alternative because laser scanning does not meet the accuracy requirements in general. A shallow Depth of Field (DoF) affects the image-based 3D reconstruction and especially the point matching procedure. This is visible not only in the total number of corresponding points but also in the resolution of the produced 3D model. The extension of the DoF is a very important task that should be incorporated in the data collection to attain a better quality of the image set and a better 3D model. An extension of the DoF can be achieved with many methods and especially with the use of the focus stacking technique. In this paper, the focus stacking technique was tested in a real-world experiment to digitise a museum artefact in 3D. The experiment conditions include the use of a full frame camera equipped with a normal lens (50mm), with the camera being placed close to the object. The artefact has already been digitised with a structured light system and that model served as the reference model in which 3D models were compared and the results were presented.

Integration of Geodata in Documenting Castle Ruins

NASA Astrophysics Data System (ADS)

Delis, P.; Wojtkowska, M.; Nerc, P.; Ewiak, I.; Lada, A.

2016-06-01

Textured three dimensional models are currently the one of the standard methods of representing the results of photogrammetric works. A realistic 3D model combines the geometrical relations between the structure's elements with realistic textures of each of its elements. Data used to create 3D models of structures can be derived from many different sources. The most commonly used tool for documentation purposes, is a digital camera and nowadays terrestrial laser scanning (TLS). Integration of data acquired from different sources allows modelling and visualization of 3D models historical structures. Additional aspect of data integration is possibility of complementing of missing points for example in point clouds. The paper shows the possibility of integrating data from terrestrial laser scanning with digital imagery and an analysis of the accuracy of the presented methods. The paper describes results obtained from raw data consisting of a point cloud measured using terrestrial laser scanning acquired from a Leica ScanStation2 and digital imagery taken using a Kodak DCS Pro 14N camera. The studied structure is the ruins of the Ilza castle in Poland.

Computer aided three-dimensional reconstruction and modeling of the pelvis, by using plastinated cross sections, as a powerful tool for morphological investigations.

PubMed

Sora, Mircea-Constantin; Jilavu, Radu; Matusz, Petru

2012-10-01

The aim of this study was to describe a method of developing a computerized model of the human female pelvis using plastinated slices. Computerized reconstruction of anatomical structures is becoming very useful for developing anatomical teaching, research modules and animations. Although databases consisting of serial sections derived from frozen cadaver material exist, plastination represents an alternative method for developing anatomical data useful for computerized reconstruction. A slice anatomy study, using plastinated transparent pelvis cross sections, was performed to obtain a 3D reconstruction. One female human pelvis used for this study, first plastinated as a block, then sliced into thin slices and in the end subjected to 3D computerized reconstruction using WinSURF modeling system (SURFdriver Software). To facilitate the understanding of the complex pelvic floor anatomy on sectional images obtained through MR imaging, and to make the representation more vivid, a female pelvis computer-aided 3D model was created. Qualitative observations revealed that the morphological features of the model were consistent with those displayed by typical cadaveric specimens. The quality of the reconstructed images appeared distinct, especially the spatial positions and complicated relationships of contiguous structures of the female pelvis. All reconstructed structures can be displayed in groups or as a whole and interactively rotated in 3D space. The utilization of plastinates for generating tissue sections is useful for 3D computerized modeling. The 3D model of the female pelvis presented in this paper provides a stereoscopic view to study the adjacent relationship and arrangement of respective pelvis sections. A better understanding of the pelvic floor anatomy is relevant to gynaecologists, radiologists, surgeons, urologists, physical therapists and all professionals who take care of women with pelvic floor dysfunction.

Fully anisotropic 3-D EM modelling on a Lebedev grid with a multigrid pre-conditioner

NASA Astrophysics Data System (ADS)

Jaysaval, Piyoosh; Shantsev, Daniil V.; de la Kethulle de Ryhove, Sébastien; Bratteland, Tarjei

2016-12-01

We present a numerical algorithm for 3-D electromagnetic (EM) simulations in conducting media with general electric anisotropy. The algorithm is based on the finite-difference discretization of frequency-domain Maxwell's equations on a Lebedev grid, in which all components of the electric field are collocated but half a spatial step staggered with respect to the magnetic field components, which also are collocated. This leads to a system of linear equations that is solved using a stabilized biconjugate gradient method with a multigrid preconditioner. We validate the accuracy of the numerical results for layered and 3-D tilted transverse isotropic (TTI) earth models representing typical scenarios used in the marine controlled-source EM method. It is then demonstrated that not taking into account the full anisotropy of the conductivity tensor can lead to misleading inversion results. For synthetic data corresponding to a 3-D model with a TTI anticlinal structure, a standard vertical transverse isotropic (VTI) inversion is not able to image a resistor, while for a 3-D model with a TTI synclinal structure it produces a false resistive anomaly. However, if the VTI forward solver used in the inversion is replaced by the proposed TTI solver with perfect knowledge of the strike and dip of the dipping structures, the resulting resistivity images become consistent with the true models.

Resistivity imaging of Aluto-Langano geothermal field using 3-D magnetotelluric inversion

NASA Astrophysics Data System (ADS)

Cherkose, Biruk Abera; Mizunaga, Hideki

2018-03-01

Magnetotelluric (MT) method is a widely used geophysical method in geothermal exploration. It is used to image subsurface resistivity structures from shallow depths up to several kilometers of depth. Resistivity imaging using MT method in high-enthalpy geothermal systems is an effective tool to identify conductive clay layers that cover the geothermal systems and to detect a potential reservoir. A resistivity model is vital for deciding the location of pilot and production sites at the early stages of a geothermal project. In this study, a 3-D resistivity model of Aluto-Langano geothermal field was constructed to map structures related to a geothermal resource. The inversion program, ModEM was used to recover the 3-D resistivity model of the study area. The 3-D inversion result revealed the three main resistivity structures: a high-resistivity surface layer related to unaltered volcanic rocks at shallow depth, underlain by a conductive zone associated with the presence of conductive clay minerals, predominantly smectite. Beneath the conductive layer, the resistivity increases gradually to higher values related to the formation of high-temperature alteration minerals such as chlorite and epidote. The resistivity model recovered from 3-D inversion in Aluto-Langano corresponds very well to the conceptual model for high-enthalpy volcanic geothermal systems. The conductive clay cap is overlying the resistive propylitic upflow zone as confirmed by the geothermal wells in the area.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shafer, Morgan W; Battaglia, D. J.; Unterberg, Ezekial A

A new tangential 2D Soft X-Ray Imaging System (SXRIS) is being designed to examine the edge magnetic island structure in the lower X-point region of DIII-D. A synthetic diagnostic calculation coupled to 3D emissivity estimates is used to generate phantom images. Phillips-Tikhonov regularization is used to invert the phantom images for comparison to the original emissivity model. Noise level, island size, and equilibrium accuracy are scanned to assess the feasibility of detecting edge island structures. Models of typical DIII-D discharges indicate integration times > 1 ms with accurate equilibrium reconstruction are needed for small island (< 3 cm) detection.

Delta: a new web-based 3D genome visualization and analysis platform.

PubMed

Tang, Bixia; Li, Feifei; Li, Jing; Zhao, Wenming; Zhang, Zhihua

2018-04-15

Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the genome. It then generates a physical 3D model which represents the plausible consensus 3D structure of the genome. Delta features a highly interactive visualization tool which enhances the integration of genome topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. Finally, by visually comparing the 3D model of the β-globin gene locus and its annotation, we speculated a plausible transitory interaction pattern in the locus. Experimental evidence was found to support this speculation by literature survey. This served as an example of intuitive hypothesis testing with the help of Delta. Delta is freely accessible from http://delta.big.ac.cn, and the source code is available at https://github.com/zhangzhwlab/delta. zhangzhihua@big.ac.cn. Supplementary data are available at Bioinformatics online.

Obtaining valid geologic models from 3-D resistivity inversion of magnetotelluric data at Pahute Mesa, Nevada

USGS Publications Warehouse

Rodriguez, Brian D.; Sweetkind, Donald S.

2015-01-01

The 3-D inversion was generally able to reproduce the gross resistivity structure of the “known” model, but the simulated conductive volcanic composite unit horizons were often too shallow when compared to the “known” model. Additionally, the chosen computation parameters such as station spacing appear to have resulted in computational artifacts that are difficult to interpret but could potentially be removed with further refinements of the 3-D resistivity inversion modeling technique.

An integrated geophysical study of the lithospheric structure beneath Libya

NASA Astrophysics Data System (ADS)

Brown, Wesley A.

This doctoral dissertation constitutes an integrated geophysical investigation of the lithospheric structure in the region of Libya. It is separated into three sections, each of which will be submitted to different scientific journals for publication. In the first part of the study, I utilized a seamless mosaicking approach based on the commercial Environment for Visualizing Images (ENVI) software package to create mosaics of two geologically interesting portions of Libya. In this study I present a step by step method of mosaicking Landsat 4 satellite images. Firstly, I performed histogram matching to give images the same color scale, then I used a cutline feathering technique to blend suture areas and finally I overlaid the images to form the two mosaics. The resulting mosaics were then combined with structural features and the seismicity map of the area. The resulting mosaics were proven to be useful in identifying recently active faults and shows great potential for verification of other faults and in natural hazard assessment. For the second portion of my research, I made use of over 6,000 free air corrected gravity data in conjunction with other geological and geophysical data to develop a 3D density model for northern Libya. I used a gravity modeling program (SURFGRAV) to develop the 3D density model by manipulating it to accurately predict large areas of Free Air anomaly shown in the data. The residual gravity anomaly values were calculated by subtracting predicted Free Air anomaly from the observed Free Air anomaly. The results were satisfactory for uplifted areas of Libya while there were significant mismatches in basin areas. The density model was iterated and used as a starting model for the final portion of the study. In the last part of this research, I used the Nafe-Drake relationship along with other geological data to convert the 3D density model to a 3D velocity model (LIBYA3D) for the region. Two earthquakes having source receiver paths sampling much of the modeled area were used to perform 1D and 1.5D validation tests, and the results were compared to those from previous studies. The results showed that the new 3D velocity model is valid and superior to the global model. However, until there is sufficient earthquake data acquired, and we are able to perform 2D and 3D modeling we may not be able to see the true improvement of LIBYA3D as compared to the other regional models.

Application of laser scanning confocal microscopy in the soft tissue exquisite structure for 3D scan

PubMed Central

Zhang, Zhaoqiang; Ibrahim, Mohamed; Fu, Yang; Wu, Xujia; Ren, Fei; Chen, Lei

2018-01-01

Three-dimensional (3D) printing is a new developing technology for printing individualized materials swiftly and precisely in the field of biological medicine (especially tissue-engineered materials). Prior to printing, it is necessary to scan the structure of the natural biological tissue, then construct the 3D printing digital model through optimizing the scanned data. By searching the literatures, magazines at home and abroad, this article reviewed the current status, main processes and matters needing attention of confocal laser scanning microscope (LSCM) in the application of soft tissue fine structure 3D scanning, empathizing the significance of LSCM in this field. PMID:29755838

Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17).

PubMed

Pramanik, Subrata; Kutzner, Arne; Heese, Klaus

2015-01-01

FAM72A (p17) is a novel neuronal protein that has been linked to tumorigenic effects in non-neuronal tissue. Using state of the art in silico physicochemical analyses (e.g., I-TASSER, RaptorX, and Modeller), we determined the three-dimensional (3D) protein structure of FAM72A and further identified potential ligand-protein interactions. Our data indicate a Zn(2+)/Fe(3+)-containing 3D protein structure, based on a 3GA3_A model template, which potentially interacts with the organic molecule RSM ((2s)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl] butanamide). The discovery of RSM may serve as potential lead for further anti-FAM72A drug screening tests in the pharmaceutical industry because interference with FAM72A's activities via RSM-related molecules might be a novel option to influence the tumor suppressor protein p53 signaling pathways for the treatment of various types of cancers.

Interactive 3D-PDF Presentations for the Simulation and Quantification of Extended Endoscopic Endonasal Surgical Approaches.

PubMed

Mavar-Haramija, Marija; Prats-Galino, Alberto; Méndez, Juan A Juanes; Puigdelívoll-Sánchez, Anna; de Notaris, Matteo

2015-10-01

A three-dimensional (3D) model of the skull base was reconstructed from the pre- and post-dissection head CT images and embedded in a Portable Document Format (PDF) file, which can be opened by freely available software and used offline. The CT images were segmented using a specific 3D software platform for biomedical data, and the resulting 3D geometrical models of anatomical structures were used for dual purpose: to simulate the extended endoscopic endonasal transsphenoidal approaches and to perform the quantitative analysis of the procedures. The analysis consisted of bone removal quantification and the calculation of quantitative parameters (surgical freedom and exposure area) of each procedure. The results are presented in three PDF documents containing JavaScript-based functions. The 3D-PDF files include reconstructions of the nasal structures (nasal septum, vomer, middle turbinates), the bony structures of the anterior skull base and maxillofacial region and partial reconstructions of the optic nerve, the hypoglossal and vidian canals and the internal carotid arteries. Alongside the anatomical model, axial, sagittal and coronal CT images are shown. Interactive 3D presentations were created to explain the surgery and the associated quantification methods step-by-step. The resulting 3D-PDF files allow the user to interact with the model through easily available software, free of charge and in an intuitive manner. The files are available for offline use on a personal computer and no previous specialized knowledge in informatics is required. The documents can be downloaded at http://hdl.handle.net/2445/55224 .

Three-Dimensional Accuracy of Facial Scan for Facial Deformities in Clinics: A New Evaluation Method for Facial Scanner Accuracy.

PubMed

Zhao, Yi-Jiao; Xiong, Yu-Xue; Wang, Yong

2017-01-01

In this study, the practical accuracy (PA) of optical facial scanners for facial deformity patients in oral clinic was evaluated. Ten patients with a variety of facial deformities from oral clinical were included in the study. For each patient, a three-dimensional (3D) face model was acquired, via a high-accuracy industrial "line-laser" scanner (Faro), as the reference model and two test models were obtained, via a "stereophotography" (3dMD) and a "structured light" facial scanner (FaceScan) separately. Registration based on the iterative closest point (ICP) algorithm was executed to overlap the test models to reference models, and "3D error" as a new measurement indicator calculated by reverse engineering software (Geomagic Studio) was used to evaluate the 3D global and partial (upper, middle, and lower parts of face) PA of each facial scanner. The respective 3D accuracy of stereophotography and structured light facial scanners obtained for facial deformities was 0.58±0.11 mm and 0.57±0.07 mm. The 3D accuracy of different facial partitions was inconsistent; the middle face had the best performance. Although the PA of two facial scanners was lower than their nominal accuracy (NA), they all met the requirement for oral clinic use.

Hormonal regulation of epithelial organization in a three-dimensional breast tissue culture model.

PubMed

Speroni, Lucia; Whitt, Gregory S; Xylas, Joanna; Quinn, Kyle P; Jondeau-Cabaton, Adeline; Barnes, Clifford; Georgakoudi, Irene; Sonnenschein, Carlos; Soto, Ana M

2014-01-01

The establishment of hormone target breast cells in the 1970's resulted in suitable models for the study of hormone control of cell proliferation and gene expression using two-dimensional (2D) cultures. However, to study mammogenesis and breast tumor development in vitro, cells must be able to organize in three-dimensional (3D) structures like in the tissue. We now report the development of a hormone-sensitive 3D culture model for the study of mammogenesis and neoplastic development. Hormone-sensitive T47D breast cancer cells respond to estradiol in a dose-dependent manner by forming complex epithelial structures. Treatment with the synthetic progestagen promegestone, in the presence of estradiol, results in flat epithelial structures that display cytoplasmic projections, a phenomenon reported to precede side-branching. Additionally, as in the mammary gland, treatment with prolactin in the presence of estradiol induces budding structures. These changes in epithelial organization are accompanied by collagen remodeling. Collagen is the major acellular component of the breast stroma and an important player in tumor development and progression. Quantitative analysis of second harmonic generation of collagen fibers revealed that collagen density was more variable surrounding budding and irregularly shaped structures when compared to more regular structures; suggesting that fiber organization in the former is more anisotropic than in the latter. In sum, this new 3D model recapitulates morphogenetic events modulated by mammogenic hormones in the breast, and is suitable for the evaluation of therapeutic agents.

LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

PubMed

González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

2012-03-01

Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

Surface reconstruction of GaAs(001) nitrided under the controlled As partial pressure [rapid communication

NASA Astrophysics Data System (ADS)

Imayoshi, Takahiro; Oigawa, Haruhiro; Shigekawa, Hidemi; Tokumoto, Hiroshi

2003-08-01

Under the controlled As partial pressure, the nitridation process of GaAs(0 0 1)-(2 × 4) surface was studied using a scanning tunneling microscope (STM) combined with an electron cyclotron resonance plasma-assisted molecular beam epitaxy system. With either prolonging the nitridation time or decreasing the As partial pressure, the previously reported (3 × 3) structure with two dimers per surface cell ((3 × 3)-2D) was found to progressively convert into a new (3 × 3) structure characterized by one dimer per surface cell ((3 × 3)-1D). Reversely the exposure to arsenic transformed the structure from (3 × 3)-1D to (3 × 3)-2D, suggesting that the topmost layer is composed of As 2-dimers. Based on these STM images together with the X-ray photoelectron spectroscopy data, we propose the new As 2-dimer coverage models to explain both (3 × 3)-1D and -2D structures involving the exchange reaction of arsenic with nitrogen in the subsurface region of GaAs.

Feasibility of fabricating personalized 3D-printed bone grafts guided by high-resolution imaging

NASA Astrophysics Data System (ADS)

Hong, Abigail L.; Newman, Benjamin T.; Khalid, Arbab; Teter, Olivia M.; Kobe, Elizabeth A.; Shukurova, Malika; Shinde, Rohit; Sipzner, Daniel; Pignolo, Robert J.; Udupa, Jayaram K.; Rajapakse, Chamith S.

2017-03-01

Current methods of bone graft treatment for critical size bone defects can give way to several clinical complications such as limited available bone for autografts, non-matching bone structure, lack of strength which can compromise a patient's skeletal system, and sterilization processes that can prevent osteogenesis in the case of allografts. We intend to overcome these disadvantages by generating a patient-specific 3D printed bone graft guided by high-resolution medical imaging. Our synthetic model allows us to customize the graft for the patients' macro- and microstructure and correct any structural deficiencies in the re-meshing process. These 3D-printed models can presumptively serve as the scaffolding for human mesenchymal stem cell (hMSC) engraftment in order to facilitate bone growth. We performed highresolution CT imaging of a cadaveric human proximal femur at 0.030-mm isotropic voxels. We used these images to generate a 3D computer model that mimics bone geometry from micro to macro scale represented by STereoLithography (STL) format. These models were then reformatted to a format that can be interpreted by the 3D printer. To assess how much of the microstructure was replicated, 3D-printed models were re-imaged using micro-CT at 0.025-mm isotropic voxels and compared to original high-resolution CT images used to generate the 3D model in 32 sub-regions. We found a strong correlation between 3D-printed bone volume and volume of bone in the original images used for 3D printing (R2 = 0.97). We expect to further refine our approach with additional testing to create a viable synthetic bone graft with clinical functionality.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

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

PubMed

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

2017-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Rapid Design and Testing of Novel Gas/liquid Contacting Devices for Post-Combustion CO 2 Capture via 3D Printing - Phase II Final Technical Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panaccione, Charles; Staab, Greg; Meuleman, Erik

ION has developed a mathematically driven model for a contacting device incorporating mass transfer, heat transfer, and computational fluid dynamics. This model is based upon a parametric structure for purposes of future commercialization. The most promising design from modeling was 3D printed and tested in a bench scale CO 2 capture unit and compared to commercially available structured packing tested in the same unit.

Resolution analysis of finite fault source inversion using one- and three-dimensional Green's functions 1. Strong motions

USGS Publications Warehouse

Graves, R.W.; Wald, D.J.

2001-01-01

We develop a methodology to perform finite fault source inversions from strong motion data using Green's functions (GFs) calculated for a three-dimensional (3-D) velocity structure. The 3-D GFs are calculated numerically by inserting body forces at each of the strong motion sites and then recording the resulting strains along the target fault surface. Using reciprocity, these GFs can be recombined to represent the ground motion at each site for any (heterogeneous) slip distribution on the fault. The reciprocal formulation significantly reduces the required number of 3-D finite difference computations to at most 3NS, where NS is the number of strong motion sites used in the inversion. Using controlled numerical resolution tests, we have examined the relative importance of accurate GFs for finite fault source inversions which rely on near-source ground motions. These experiments use both 1-D and 3-D GFs in inversions for hypothetical rupture models in order (1) to analyze the ability of the 3-D methodology to resolve trade-offs between complex source phenomena and 3-D path effects, (2) to address the sensitivity of the inversion results to uncertainties in the 3-D velocity structure, and (3) to test the adequacy of the 1-D GF method when propagation effects are known to be three-dimensional. We find that given "data" from a prescribed 3-D Earth structure, the use of well-calibrated 3-D GFs in the inversion provides very good resolution of the assumed slip distribution, thus adequately separating source and 3-D propagation effects. In contrast, using a set of inexact 3-D GFs or a set of hybrid 1-D GFs allows only partial recovery of the slip distribution. These findings suggest that in regions of complex geology the use of well-calibrated 3-D GFs has the potential for increased resolution of the rupture process relative to 1-D GFs. However, realizing this full potential requires that the 3-D velocity model and associated GFs should be carefully validated against the true 3-D Earth structure before performing the inverse problem with actual data. Copyright 2001 by the American Geophysical Union.

G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures.

PubMed

Solomon, Oz; Kunik, Vered; Simon, Amos; Kol, Nitzan; Barel, Ortal; Lev, Atar; Amariglio, Ninette; Somech, Raz; Rechavi, Gidi; Eyal, Eran

2016-08-26

Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D . G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.

Estimation of Time Dependent Properties from Surface Pressure in Open Cavities

DTIC Science & Technology

2008-02-01

static pressure of the cavity. The stagnation and static pressures are measured separately with Druck Model DPI 145 pressure transducers (with a quoted...interacting with the ZNMF actuator jets, the 2D shape of the vortical structures transform to a 3D shape with spanwise vortical structures. These...Therefore, the pressure gradient in the d direction is dd ° 3d Substituting Equation (5.3) into Equation (5.5) results in ^l = PJk(e^-Re^)/c^ (5.6

The influence of lateral Earth structure on glacial isostatic adjustment in Greenland

NASA Astrophysics Data System (ADS)

Milne, Glenn A.; Latychev, Konstantin; Schaeffer, Andrew; Crowley, John W.; Lecavalier, Benoit S.; Audette, Alexandre

2018-05-01

We present the first results that focus on the influence of lateral Earth structure on Greenland glacial isostatic adjustment (GIA) using a model that can explicitly incorporate 3-D Earth structure. In total, eight realisations of lateral viscosity structure were developed using four global seismic velocity models and two global lithosphere (elastic) thickness models. Our results show that lateral viscosity structure has a significant influence on model output of both deglacial relative sea level (RSL) changes and present-day rates of vertical land motion. For example, lateral structure changes the RSL predictions in the Holocene by several 10 s of metres in many locations relative to the 1-D case. Modelled rates of vertical land motion are also significantly affected, with differences from the 1-D case commonly at the mm/yr level and exceeding 2 mm/yr in some locations. The addition of lateral structure was unable to account for previously identified data-model RSL misfits in northern and southern Greenland, suggesting limitations in the adopted ice model (Lecavalier et al. 2014) and/or the existence of processes not included in our model. Our results show large data-model discrepancies in uplift rates when applying a 1-D viscosity model tuned to fit the RSL data; these discrepancies cannot be reconciled by adding the realisations of lateral structure considered here. In many locations, the spread in model output for the eight different 3-D Earth models is of similar amplitude or larger than the influence of lateral structure (as defined by the average of all eight model runs). This reflects the differences between the four seismic and two lithosphere models used and implies a large uncertainty in defining the GIA signal given that other aspects that contribute to this uncertainty (e.g. scaling from seismic velocity to viscosity) were not considered in this study. In order to reduce this large model uncertainty, an important next step is to develop more accurate constraints on Earth structure beneath Greenland based on regional geophysical data sets.

Creating computer aided 3D model of spleen and kidney based on Visible Human Project.

PubMed

Aldur, Muhammet M

2005-01-01

To investigate the efficacy of computer aided 3-dimensional (3D) reconstruction technique on visualization and modeling of gross anatomical structures with an affordable methodology applied on the spleen and kidney. From The Visible Human Project Dataset cryosection images, developed by the National Library of Medicine, the spleen and kidney sections were preferred to be used due to their highly distinct contours. The software used for the reconstruction were SurfDriver 3.5.3 for Mac and Cinema 4D XL version 7.1 for Mac OS X. This study was carried out in May 2004 at the Department of Anatomy, Hacettepe University, Ankara, Turkey. As a result of this study, it is determined that these 2 programs could be effectively used both for 3D modeling of the mentioned organs and volumetric analyses on these models. It is also seen that it is possible to hold the physical models of these gross anatomical digital ones with stereolithography technique by means of the data exchange file format provided by the program and present such images as anaglyph. SurfDriver 3.5.3 for Mac OS and Cinema 4 DXL version 7.1 for Mac OS X can be used effectively for reconstruction of gross anatomical structures from serial parallel sections with distinct contours such as spleen and kidney and the animation of models. These software constitute a highly effective way of getting volumetric calculations, spatial relations and morphometrical measurements of reconstructed structures.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Three dimensional (3D) microstructure-based finite element modeling of Al-SiC nanolaminates using focused ion beam (FIB) tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Carl R.

Al-SiC nanolaminate composites show promise as high performance coating materials due to their combination of strength and toughness. Although a significant amount of modeling effort has been focused on materials with an idealized flat nanostructure, experimentally these materials exhibit complex undulating layer geometries. This work utilizes FIB tomography to characterize this nanostructure in 3D and finite element modeling to determine the effect that this complex structure has on the mechanical behavior of these materials. A sufficiently large volume was characterized such that a 1 × 2 μm micropillar could be generated from the dataset and compared directly to experimental results.more » The mechanical response from this nanostructure was then compared to pillar models using simplified structures with perfectly flat layers, layers with sinusoidal waviness, and layers with arc segment waviness. The arc segment based layer geometry showed the best agreement with the experimentally determined structure, indicating it would be the most appropriate geometry for future modeling efforts. - Highlights: •FIB tomography was used to determine the structure of an Al-SiC nanolaminate in 3D. •FEM was used to compare the deformation of the nanostructure to experimental results. •Idealized structures from literature were compared to the FIB determined structure. •Arc segment based structures approximated the FIB determined structure most closely.« less

Numerical investigation of band gaps in 3D printed cantilever-in-mass metamaterials

NASA Astrophysics Data System (ADS)

Qureshi, Awais; Li, Bing; Tan, K. T.

2016-06-01

In this research, the negative effective mass behavior of elastic/mechanical metamaterials is exhibited by a cantilever-in-mass structure as a proposed design for creating frequency stopping band gaps, based on local resonance of the internal structure. The mass-in-mass unit cell model is transformed into a cantilever-in-mass model using the Bernoulli-Euler beam theory. An analytical model of the cantilever-in-mass structure is derived and the effects of geometrical dimensions and material parameters to create frequency band gaps are examined. A two-dimensional finite element model is created to validate the analytical results, and excellent agreement is achieved. The analytical model establishes an easily tunable metamaterial design to realize wave attenuation based on locally resonant frequency. To demonstrate feasibility for 3D printing, the analytical model is employed to design and fabricate 3D printable mechanical metamaterial. A three-dimensional numerical experiment is performed using COMSOL Multiphysics to validate the wave attenuation performance. Results show that the cantilever-in-mass metamaterial is capable of mitigating stress waves at the desired resonance frequency. Our study successfully presents the use of one constituent material to create a 3D printed cantilever-in-mass metamaterial with negative effective mass density for stress wave mitigation purposes.

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

NASA Astrophysics Data System (ADS)

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

2008-09-01

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

A 3-dimensional human embryonic stem cell (hESC)-derived model to detect developmental neurotoxicity of nanoparticles.

PubMed

Hoelting, Lisa; Scheinhardt, Benjamin; Bondarenko, Olesja; Schildknecht, Stefan; Kapitza, Marion; Tanavde, Vivek; Tan, Betty; Lee, Qian Yi; Mecking, Stefan; Leist, Marcel; Kadereit, Suzanne

2013-04-01

Nanoparticles (NPs) have been shown to accumulate in organs, cross the blood-brain barrier and placenta, and have the potential to elicit developmental neurotoxicity (DNT). Here, we developed a human embryonic stem cell (hESC)-derived 3-dimensional (3-D) in vitro model that allows for testing of potential developmental neurotoxicants. Early central nervous system PAX6(+) precursor cells were generated from hESCs and differentiated further within 3-D structures. The 3-D model was characterized for neural marker expression revealing robust differentiation toward neuronal precursor cells, and gene expression profiling suggested a predominantly forebrain-like development. Altered neural gene expression due to exposure to non-cytotoxic concentrations of the known developmental neurotoxicant, methylmercury, indicated that the 3-D model could detect DNT. To test for specific toxicity of NPs, chemically inert polyethylene NPs (PE-NPs) were chosen. They penetrated deep into the 3-D structures and impacted gene expression at non-cytotoxic concentrations. NOTCH pathway genes such as HES5 and NOTCH1 were reduced in expression, as well as downstream neuronal precursor genes such as NEUROD1 and ASCL1. FOXG1, a patterning marker, was also reduced. As loss of function of these genes results in severe nervous system impairments in mice, our data suggest that the 3-D hESC-derived model could be used to test for Nano-DNT.

A novel anisotropic inversion approach for magnetotelluric data from subsurfaces with orthogonal geoelectric strike directions

NASA Astrophysics Data System (ADS)

Schmoldt, Jan-Philipp; Jones, Alan G.

2013-12-01

The key result of this study is the development of a novel inversion approach for cases of orthogonal, or close to orthogonal, geoelectric strike directions at different depth ranges, for example, crustal and mantle depths. Oblique geoelectric strike directions are a well-known issue in commonly employed isotropic 2-D inversion of MT data. Whereas recovery of upper (crustal) structures can, in most cases, be achieved in a straightforward manner, deriving lower (mantle) structures is more challenging with isotropic 2-D inversion in the case of an overlying region (crust) with different geoelectric strike direction. Thus, investigators may resort to computationally expensive and more limited 3-D inversion in order to derive the electric resistivity distribution at mantle depths. In the novel approaches presented in this paper, electric anisotropy is used to image 2-D structures in one depth range, whereas the other region is modelled with an isotropic 1-D or 2-D approach, as a result significantly reducing computational costs of the inversion in comparison with 3-D inversion. The 1- and 2-D versions of the novel approach were tested using a synthetic 3-D subsurface model with orthogonal strike directions at crust and mantle depths and their performance was compared to results of isotropic 2-D inversion. Structures at crustal depths were reasonably well recovered by all inversion approaches, whereas recovery of mantle structures varied significantly between the different approaches. Isotropic 2-D inversion models, despite decomposition of the electric impedance tensor and using a wide range of inversion parameters, exhibited severe artefacts thereby confirming the requirement of either an enhanced or a higher dimensionality inversion approach. With the anisotropic 1-D inversion approach, mantle structures of the synthetic model were recovered reasonably well with anisotropy values parallel to the mantle strike direction (in this study anisotropy was assigned to the mantle region), indicating applicability of the novel approach for basic subsurface cases. For the more complex subsurface cases, however, the anisotropic 1-D inversion approach is likely to yield implausible models of the electric resistivity distribution due to inapplicability of the 1-D approximation. Owing to the higher number of degrees of freedom, the anisotropic 2-D inversion approach can cope with more complex subsurface cases and is the recommended tool for real data sets recorded in regions with orthogonal geoelectric strike directions.

Fold-structure analysis of paleozoic rocks in the Variscan Harz Mountains (Lautenthal, Central Germany) based on laserscanning and 3D modelling

NASA Astrophysics Data System (ADS)

Wagner, Bianca; Leiss, Bernd; Stöpler, Ralf; Zahnow, Fabian

2017-04-01

Folded paleozoic sedimentary rocks of Upper Devonian to Lower Carboniferous age are very well exposed in the abandoned chert quarry of Lautenthal in the western Harz Mountains. The outcrop represents typical structures of the Rhenohercynian thrust and fold belt of the Variscan orogen and therefore allows quantitative studies for the understanding of e.g. fold mechanisms and the amount of shortening. The sequence is composed of alternating beds of cherts, shales and tuffites, which show varying thicknesses, undulating and thinning out of certain layers. Irregularly occurring lenses of greywackes are interpreted as sedimentary intrusions. The compressive deformation style is expressed by different similar and parallel fold structures at varying scales as well as small-scale reverse faults and triangle structures. An accurate mapping of the outcrop in the classical way is very challenging due to distant and unconnected outcrop parts with differing elevations and orientations. Furthermore, the visibility is limited because of nearby trees, diffuse vegetation cover and no available total view. Therefore, we used a FARO 120 3D laserscanner and Trimble GNSS device to generate a referenced and drawn to scale point cloud of the complete quarry. Based on the point cloud a geometric 3D model of prominent horizons and structural features of various sizes was constructed. Thereafter, we analyzed the structures in matters of orientation and deformation mechanisms. Finally, we applied a retrodeformation algorithm on the model to restore the original sedimentary sequence and to calculate shortening including the amount of pressure solution. Only digital mapping allows such a time-saving, accurate and especially complete 3D survey of this excellent study object. We demonstrated that such 3D-models enable spatial correlations with other complex structures cropping out in the area. Moreover, we confirmed that a structural upscaling to the 100 to 1000 m scale is much easier and much more instructive than it could have been done in the classical way.

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

ERIC Educational Resources Information Center

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

Effect of 3-D viscoelastic structure on post-seismic relaxation from the 2004 M = 9.2 Sumatra earthquake

USGS Publications Warehouse

Pollitz, F.; Banerjee, P.; Grijalva, K.; Nagarajan, B.; Burgmann, R.

2008-01-01

The 2004 M=9.2 Sumatra-Andaman earthquake profoundly altered the state of stress in a large volume surrounding the ???1400 km long rupture. Induced mantle flow fields and coupled surface deformation are sensitive to the 3-D rheology structure. To predict the post-seismic motions from this earthquake, relaxation of a 3-D spherical viscoelastic earth model is simulated using the theory of coupled normal modes. The quasi-static deformation basis set and solution on the 3-D model is constructed using: a spherically stratified viscoelastic earth model with a linear stress-strain relation; an aspherical perturbation in viscoelastic structure; a 'static'mode basis set consisting of Earth's spheroidal and toroidal free oscillations; a "viscoelastic" mode basis set; and interaction kernels that describe the coupling among viscoelastic and static modes. Application to the 2004 Sumatra-Andaman earthquake illustrates the profound modification of the post-seismic flow field at depth by a slab structure and similarly large effects on the near-field post-seismic deformation field at Earth's surface. Comparison with post-seismic GPS observations illustrates the extent to which viscoelastic relaxation contributes to the regional post-seismic deformation. ?? Journal compilation ?? 2008 RAS.

A crustal seismic velocity model for the UK, Ireland and surrounding seas

USGS Publications Warehouse

Kelly, A.; England, R.W.; Maguire, Peter K.H.

2007-01-01

A regional model of the 3-D variation in seismic P-wave velocity structure in the crust of NW Europe has been compiled from wide-angle reflection/refraction profiles. Along each 2-D profile a velocity-depth function has been digitised at 5 km intervals. These 1-D velocity functions were mapped into three dimensions using ordinary kriging with weights determined to minimise the difference between digitised and interpolated values. An analysis of variograms of the digitised data suggested a radial isotropic weighting scheme was most appropriate. Horizontal dimensions of the model cells are optimised at 40 ?? 40 km and the vertical dimension at 1 km. The resulting model provides a higher resolution image of the 3-D variation in seismic velocity structure of the UK, Ireland and surrounding areas than existing models. The construction of the model through kriging allows the uncertainty in the velocity structure to be assessed. This uncertainty indicates the high density of data required to confidently interpolate the crustal velocity structure, and shows that for this region the velocity is poorly constrained for large areas away from the input data. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

Biology Students’ Initial Mental Model about Microorganism

NASA Astrophysics Data System (ADS)

Hamdiyati, Y.; Sudargo, F.; Redjeki, S.; Fitriani, A.

2017-02-01

The purpose of this study was to identify biology students’ initial mental model about microorganism. This research used descriptive method with 32 sixth semester biology students at Biology Education Departement-Universitas Pendidikan Indonesia as its respondents. Data was taken at the beginning of the 6th semester before respondents endure microbiology course. Instrument used to assess mental model was drawing-writing test in which it contains concepts such as structure of bacteria, archaea, virus, and fungi. Students were asked to describe their imagination about the structure of microorganisms and subsequently asked to explain the structure of microorganisms in writing through open-ended questions. Students’ response was then compared to scientists or experts’ mental models as the targeted mental model. Student mental models were categorized into five levels (levels 1-5), namely “there is no drawing/writing,” “wrong or irrelevant drawing/writing of question,” “partially correct drawing/writing,” “the drawing/writing that has some deficiencies,” and “completely correct and complete drawing/writing.” Results showed that the level of mental models through drawing or writing about the four concepts were varied. The highest level of mental models through drawing (D5) was found in the concept of bacteria, while the highest level of mental models through writing (W3) was found in the concept of bacteria, virus, and fungi. Mental model levels most commonly found in each concept through drawing-writing tests (D/W) were bacteria (D2/W2), Archaea (D1/W1 and D2/W2), virus (D3/W3), and fungi (D2/W1). From these results it is advisable to improve lectures and assessment strategy to enhance or complement students’ mental models about microorganisms.

The 3D Reference Earth Model (REM-3D): Update and Outlook

NASA Astrophysics Data System (ADS)

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

2016-12-01

Elastic properties of the Earth's interior (e.g. density, rigidity, compressibility, anisotropy) vary spatially due to changes in temperature, pressure, composition, and flow. In the 20th century, seismologists have constructed reference models of how these quantities vary with depth, notably the PREM model of Dziewonski and Anderson (1981). These 1D reference earth models have proven indispensable in earthquake location, imaging of interior structure, understanding material properties under extreme conditions, and as a reference in other fields, such as particle physics and astronomy. Over the past three decades, more sophisticated efforts by seismologists have yielded several generations of models of how properties vary not only with depth, but also laterally. Yet, though these three-dimensional (3D) models exhibit compelling similarities at large scales, differences in the methodology, representation of structure, and dataset upon which they are based, have prevented the creation of 3D community reference models. We propose to overcome these challenges by compiling, reconciling, and distributing a long period (>15 s) reference seismic dataset, from which we will construct a 3D seismic reference model (REM-3D) for the Earth's mantle, which will come in two flavors: a long wavelength smoothly parameterized model and a set of regional profiles. Here, we summarize progress made in the construction of the reference long period dataset, and present preliminary versions of the REM-3D in order to illustrate the two flavors of REM-3D and their relative advantages and disadvantages. As a community reference model and with fully quantified uncertainties and tradeoffs, REM-3D will facilitate Earth imaging studies, earthquake characterization, inferences on temperature and composition in the deep interior, and be of improved utility to emerging scientific endeavors, such as neutrino geoscience. In this presentation, we outline the outlook for setting up advisory community working groups and the community workshop that would assess progress, evaluate model and dataset performance, identify avenues for improvement, and recommend strategies for maximizing model adoption in and utility for the deep Earth community.

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…

A Downloadable Three-Dimensional Virtual Model of the Visible Ear

PubMed Central

Wang, Haobing; Merchant, Saumil N.; Sorensen, Mads S.

2008-01-01

Purpose To develop a three-dimensional (3-D) virtual model of a human temporal bone and surrounding structures. Methods A fresh-frozen human temporal bone was serially sectioned and digital images of the surface of the tissue block were recorded (the ‘Visible Ear’). The image stack was resampled at a final resolution of 50 × 50 × 50/100 µm/voxel, registered in custom software and segmented in PhotoShop® 7.0. The segmented image layers were imported into Amira® 3.1 to generate smooth polygonal surface models. Results The 3-D virtual model presents the structures of the middle, inner and outer ears in their surgically relevant surroundings. It is packaged within a cross-platform freeware, which allows for full rotation, visibility and transparency control, as well as the ability to slice the 3-D model open at any section. The appropriate raw image can be superimposed on the cleavage plane. The model can be downloaded at https://research.meei.harvard.edu/Otopathology/3dmodels/ PMID:17124433

3D-Printing Crystallographic Unit Cells for Learning Materials Science and Engineering

ERIC Educational Resources Information Center

Rodenbough, Philip P.; Vanti, William B.; Chan, Siu-Wai

2015-01-01

Introductory materials science and engineering courses universally include the study of crystal structure and unit cells, which are by their nature highly visual 3D concepts. Traditionally, such topics are explored with 2D drawings or perhaps a limited set of difficult-to-construct 3D models. The rise of 3D printing, coupled with the wealth of…

A validation test for Adagio through replication of Big Hill and Bayou Choctaw JAS3D models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Byoung Yoon

2013-06-01

JAS3D, a three dimensional iterative solid mechanics code, has been used for structural analyses for the Strategic Petroleum Reserve system since the 1990s. JAS3D is no longer supported by Sandia National Laboratories, and has been replaced by Adagio. To validate the transition from JAS3D to Adagio, the existing JAS3D input decks and user subroutines for Bayou Choctaw and Big Hill models were converted for use with Adagio. The calculation results from the Adagio runs are compared to the JAS3D. Since the Adagio results are very similar to the JAS3D results, Adagio is judged to be performing satisfactorily.

Action detection by double hierarchical multi-structure space-time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-03-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

Action detection by double hierarchical multi-structure space–time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-06-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

The future of structural fieldwork - UAV assisted aerial photogrammetry

NASA Astrophysics Data System (ADS)

Vollgger, Stefan; Cruden, Alexander

2015-04-01

Unmanned aerial vehicles (UAVs), commonly referred to as drones, are opening new and low cost possibilities to acquire high-resolution aerial images and digital surface models (DSM) for applications in structural geology. UAVs can be programmed to fly autonomously along a user defined grid to systematically capture high-resolution photographs, even in difficult to access areas. The photographs are subsequently processed using software that employ SIFT (scale invariant feature transform) and SFM (structure from motion) algorithms. These photogrammetric routines allow the extraction of spatial information (3D point clouds, digital elevation models, 3D meshes, orthophotos) from 2D images. Depending on flight altitude and camera setup, sub-centimeter spatial resolutions can be achieved. By "digitally mapping" georeferenced 3D models and images, orientation data can be extracted directly and used to analyse the structural framework of the mapped object or area. We present UAV assisted aerial mapping results from a coastal platform near Cape Liptrap (Victoria, Australia), where deformed metasediments of the Palaeozoic Lachlan Fold Belt are exposed. We also show how orientation and spatial information of brittle and ductile structures extracted from the photogrammetric model can be linked to the progressive development of folds and faults in the region. Even though there are both technical and legislative limitations, which might prohibit the use of UAVs without prior commercial licensing and training, the benefits that arise from the resulting high-resolution, photorealistic models can substantially contribute to the collection of new data and insights for applications in structural geology.

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

Review of 3d GIS Data Fusion Methods and Progress

NASA Astrophysics Data System (ADS)

Hua, Wei; Hou, Miaole; Hu, Yungang

2018-04-01

3D data fusion is a research hotspot in the field of computer vision and fine mapping, and plays an important role in fine measurement, risk monitoring, data display and other processes. At present, the research of 3D data fusion in the field of Surveying and mapping focuses on the 3D model fusion of terrain and ground objects. This paper summarizes the basic methods of 3D data fusion of terrain and ground objects in recent years, and classified the data structure and the establishment method of 3D model, and some of the most widely used fusion methods are analysed and commented.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

The Vajont rockslide has been the object of several studies because of its catastrophic consequences and particular evolution. Several qualitative or quantitative models have been presented in the last 50 years, but a complete explanation of all relevant geological and mechanical processes remains elusive. In order to better understand the mechanics and dynamics of the 1963 event, we have reconstructed the first 3D geological model of the rockslide, which allowed us to accurately investigate the rockslide structure and kinematics. The input data for the model consisted in: pre- and post-rockslide geological maps, pre- and post-rockslide orthophotos, pre- and post-rockslide digital elevation models, structural data, boreholes, and geophysical data (2D and 3D seismics and resistivity). All these data have been integrated in a 3D geological model implemented in Gocad®, using the implicit surface modelling method. Results of the 3D geological model include the depth and geometry of the sliding surface, the volume of the two lobes of the rockslide accumulation, kinematics of the rockslide in terms of the vector field of finite displacement, and high quality meshes useful for mechanical and hydrogeological simulations. The latter can include information about the stratigraphy and internal structure of the rock masses and allow tracing the displacement of different material points in the rockslide from the pre-1963-failure to the post-rockslide state. As a general geological conclusion, we may say that the 3D model allowed us to recognize very effectively a sliding surface, whose non-planar geometry is affected by the interference pattern of two regional-scale fold systems. The rockslide is partitioned into two distinct and internally continuous rock masses with a distinct kinematics, which were characterised by a very limited internal deformation during the slide. The continuity of these two large blocks points to a very localized deformation, occurring along a thin, continuous and weak cataclastic horizon. The chosen modelling strategy, based on both traditional "explicit" and implicit techniques, was found to be very effective for reconstructing complex folded and faulted geological structures, and could be applied also to other geological environments. Finally 3D FEM analyses using the code MidasGTS have been performed adopting the 3D geological model. A c-phi reduction procedure was employed along the pre-defined failure surface until the onset of the landslide occurred. The initiation of the rock mass movements is properly described by considering the evolution of plastic shear strain in the failure surface. The stress, strain and displacement fields of the rock mass were analysed in detail and compared with the monitored data.

A model of the complex between human {beta}-microseminoprotein and CRISP-3 based on NMR data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghasriani, Houman; Fernlund, Per; Udby, Lene

2009-01-09

{beta}-Microseminoprotein (MSP), a 10 kDa seminal plasma protein, forms a tight complex with cysteine-rich secretory protein 3 (CRISP-3) from granulocytes. The 3D structure of human MSP has been determined but there is as yet no 3D structure for CRISP-3. We have now studied the complex between human MSP and CRISP-3 with multidimensional NMR. {sup 15}N-HSQC spectra show substantial differences between free and complexed hMSP. Using several 3D-NMR spectra of triply labeled hMSP in complex with a recombinant N-terminal domain of CRISP-3, most of the backbone of hMSP could be assigned. The data show that only one side of hMSP, comprisingmore » {beta}-strands 1, 4, 5, and 8 are affected by the complex formation, indicating that {beta}-strands 1 and 8 form the main binding surface. Based on this we present a tentative structure for the hMSP-CRISP-3 complex using the known crystal structure of triflin as a model of CRISP-3.« less

Using Computer-Aided Design Software and 3D Printers to Improve Spatial Visualization

ERIC Educational Resources Information Center

Katsio-Loudis, Petros; Jones, Millie

2015-01-01

Many articles have been published on the use of 3D printing technology. From prefabricated homes and outdoor structures to human organs, 3D printing technology has found a niche in many fields, but especially education. With the introduction of AutoCAD technical drawing programs and now 3D printing, learners can use 3D printed models to develop…

Study on the activity of non-purine xanthine oxidase inhibitor by 3D-QSAR modeling and molecular docking

NASA Astrophysics Data System (ADS)

Li, Peizhen; Tian, Yueli; Zhai, Honglin; Deng, Fangfang; Xie, Meihong; Zhang, Xiaoyun

2013-11-01

Non-purine derivatives have been shown to be promising novel drug candidates as xanthine oxidase inhibitors. Based on three-dimensional quantitative structure-activity relationship (3D-QSAR) methods including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), two 3D-QSAR models for a series of non-purine xanthine oxidase (XO) inhibitors were established, and their reliability was supported by statistical parameters. Combined 3D-QSAR modeling and the results of molecular docking between non-purine xanthine oxidase inhibitors and XO, the main factors that influenced activity of inhibitors were investigated, and the obtained results could explain known experimental facts. Furthermore, several new potential inhibitors with higher activity predicted were designed, which based on our analyses, and were supported by the simulation of molecular docking. This study provided some useful information for the development of non-purine xanthine oxidase inhibitors with novel structures.

Chemometric modeling of 5-Phenylthiophenecarboxylic acid derivatives as anti-rheumatic agents.

PubMed

Adhikari, Nilanjan; Jana, Dhritiman; Halder, Amit K; Mondal, Chanchal; Maiti, Milan K; Jha, Tarun

2012-09-01

Arthritis involves joint inflammation, synovial proliferation and damage of cartilage. Interleukin-1 undergoes acute and chronic inflammatory mechanisms of arthritis. Non-steroidal anti-inflammatory drugs can produce symptomatic relief but cannot act through mechanisms of arthritis. Diseases modifying anti-rheumatoid drugs reduce the symptoms of arthritis like decrease in pain and disability score, reduction of swollen joints, articular index and serum concentration of acute phage proteins. Recently, some literature references are obtained on molecular modeling of antirheumatic agents. We have tried chemometric modeling through 2D-QSAR studies on a dataset of fifty-one compounds out of which forty-four 5-Phenylthiophenecarboxylic acid derivatives have IL-1 inhibitory activity and forty-six 5-Phenylthiophenecarboxylic acid derivatives have %AIA suppressive activity. The work was done to find out the structural requirements of these anti-rheumatic agents. 2D QSAR models were generated by 2D and 3D descriptors by using multiple linear regression and partial least square method where IL-1 antagonism was considered as the biological activity parameter. Statistically significant models were developed on the training set developed by k-means cluster analysis. Sterimol parameters, electronic interaction at atom number 9, 2D autocorrelation descriptors, information content descriptor, average connectivity index chi-3, radial distribution function, Balaban 3D index and 3D-MoRSE descriptors were found to play crucial roles to modulate IL-1 inhibitory activity. 2D autocorrelation descriptors like Broto-Moreau autocorrelation of topological structure-lag 3 weighted by atomic van der Waals volumes, Geary autocorrelation-lag 7 associated with weighted atomic Sanderson electronegativities and 3D-MoRSE descriptors like 3D-MoRSE-signal 22 related to atomic van der Waals volumes, 3D-MoRSE-signal 28 related to atomic van der Waals volumes and 3D-MoRSE-signal 9 which was unweighted, were found to play important roles to model %AIA suppressive activity.

3D modeling of a dolerite intrusion from the photogrammetric and geophysical data integration.

NASA Astrophysics Data System (ADS)

Duarte, João; Machadinho, Ana; Figueiredo, Fernando; Mira, Maria

2015-04-01

The aims of this study is create a methodology based on the integration of data obtained from various available technologies, which allow a credible and complete evaluation of rock masses. In this particular case of a dolerite intrusion, which deployed an exploration of aggregates and belongs to the Jobasaltos - Extracção e Britagem. S.A.. Dolerite intrusion is situated in the volcanic complex of Serra de Todo-o-Mundo, Casais Gaiola, intruded in Jurassic sandstones. The integration of the surface and subsurface mapping, obtained by technology UAVs (Drone) and geophysical surveys (Electromagnetic Method - TEM 48 FAST), allows the construction of 2D and 3D models of the study local. The combination of the 3D point clouds produced from two distinct processes, modeling of photogrammetric and geophysical data, will be the basis for the construction of a single model of set. The rock masses in an integral perspective being visible their development above the surface and subsurface. The presentation of 2D and 3D models will give a perspective of structures, fracturation, lithology and their spatial correlations contributing to a better local knowledge, as well as its potential for the intended purpose. From these local models it will be possible to characterize and quantify the geological structures. These models will have its importance as a tool to assist in the analysis and drafting of regional models. The qualitative improvement in geological/structural modeling, seeks to reduce the value of characterization/cost ratio, in phase of prospecting, improving the investment/benefit ratio. This methodology helps to assess more accurately the economic viability of the projects.

3D Printing of Molecular Models with Calculated Geometries and p Orbital Isosurfaces

ERIC Educational Resources Information Center

Carroll, Felix A.; Blauch, David N.

2017-01-01

3D printing was used to prepare models of the calculated geometries of unsaturated organic structures. Incorporation of p orbital isosurfaces into the models enables students in introductory organic chemistry courses to have hands-on experience with the concept of orbital alignment in strained and unstrained p systems.

Computer-aided design of microvasculature systems for use in vascular scaffold production.

PubMed

Mondy, William Lafayette; Cameron, Don; Timmermans, Jean-Pierre; De Clerck, Nora; Sasov, Alexander; Casteleyn, Christophe; Piegl, Les A

2009-09-01

In vitro biomedical engineering of intact, functional vascular networks, which include capillary structures, is a prerequisite for adequate vascular scaffold production. Capillary structures are necessary since they provide the elements and compounds for the growth, function and maintenance of 3D tissue structures. Computer-aided modeling of stereolithographic (STL) micro-computer tomographic (micro-CT) 3D models is a technique that enables us to mimic the design of vascular tree systems containing capillary beds, found in tissues. In our first paper (Mondy et al 2009 Tissue Eng. at press), using micro-CT, we studied the possibility of using vascular tissues to produce data capable of aiding the design of vascular tree scaffolding, which would help in the reverse engineering of a complete vascular tree system including capillary bed structures. In this paper, we used STL models of large datasets of computer-aided design (CAD) data of vascular structures which contained capillary structures that mimic those in the dermal layers of rabbit skin. Using CAD software we created from 3D STL models a bio-CAD design for the development of capillary-containing vascular tree scaffolding for skin. This method is designed to enhance a variety of therapeutic protocols including, but not limited to, organ and tissue repair, systemic disease mediation and cell/tissue transplantation therapy. Our successful approach to in vitro vasculogenesis will allow the bioengineering of various other types of 3D tissue structures, and as such greatly expands the potential applications of biomedical engineering technology into the fields of biomedical research and medicine.

The limits of hamiltonian structures in three-dimensional elasticity, shells, and rods

NASA Astrophysics Data System (ADS)

Ge, Z.; Kruse, H. P.; Marsden, J. E.

1996-01-01

This paper uses Hamiltonian structures to study the problem of the limit of three-dimensional (3D) elastic models to shell and rod models. In the case of shells, we show that the Hamiltonian structure for a three-dimensional elastic body converges, in a sense made precise, to that for a shell model described by a one-director Cosserat surface as the thickness goes to zero. We study limiting procedures that give rise to unconstrained as well as constrained Cosserat director models. The case of a rod is also considered and similar convergence results are established, with the limiting model being a geometrically exact director rod model (in the framework developed by Antman, Simo, and coworkers). The resulting model may or may not have constraints, depending on the nature of the constitutive relations and their behavior under the limiting procedure. The closeness of Hamiltonian structures is measured by the closeness of Poisson brackets on certain classes of functions, as well as the Hamiltonians. This provides one way of justifying the dynamic one-director model for shells. Another way of stating the convergence result is that there is an almost-Poisson embedding from the phase space of the shell to the phase space of the 3D elastic body, which implies that, in the sense of Hamiltonian structures, the dynamics of the elastic body is close to that of the shell. The constitutive equations of the 3D model and their behavior as the thickness tends to zero dictates whether the limiting 2D model is a constrained or an unconstrained director model. We apply our theory in the specific case of a 3D Saint Venant-Kirchhoff material and derive the corresponding limiting shell and rod theories. The limiting shell model is an interesting Kirchhoff-like shell model in which the stored energy function is explicitly derived in terms of the shell curvature. For rods, one gets (with an additional inextensibility constraint) a one-director Kirchhoff elastic rod model, which reduces to the well-known Euler elastica if one adds an additional single constraint that the director lines up with the Frenet frame.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

The 3D Reference Earth Model: Status and Preliminary Results

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

PubMed Central

Hinton, Thomas J.; Jallerat, Quentin; Palchesko, Rachelle N.; Park, Joon Hyung; Grodzicki, Martin S.; Shue, Hao-Jan; Ramadan, Mohamed H.; Hudson, Andrew R.; Feinberg, Adam W.

2015-01-01

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

Producing genome structure populations with the dynamic and automated PGS software.

PubMed

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank

2018-05-01

Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genome's organization in space and time. We provide a user-friendly software package, called PGS, which runs on local machines (for practice runs) and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix, along with information about genome segmentation, and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and provides tools to extract and analyze the 3D coordinates of specific domains. Basic Linux command-line knowledge is sufficient for using this software. A typical running time of the pipeline is ∼3 d with 300 cores on a computer cluster to generate a population of 1,000 diploid genome structures at topological-associated domain (TAD)-level resolution.

Is a Three-Dimensional Printing Model Better Than a Traditional Cardiac Model for Medical Education? A Pilot Randomized Controlled Study.

PubMed

Wang, Zhongmin; Liu, Yuhao; Luo, Hongxing; Gao, Chuanyu; Zhang, Jing; Dai, Yuya

2017-11-01

Three-dimensional (3D) printing is a newly-emerged technology converting a series of two-dimensional images to a touchable 3D model, but no studies have investigated whether or not a 3D printing model is better than a traditional cardiac model for medical education. A 3D printing cardiac model was generated using multi-slice computed tomography datasets. Thirty-four medical students were randomized to either the 3D Printing Group taught with the aid of a 3D printing cardiac model or the Traditional Model Group with a commonly used plastic cardiac model. Questionnaires with 10 medical questions and 3 evaluative questions were filled in by the students. A 3D printing cardiac model was successfully generated. Students in the 3D Printing Group were slightly quicker to answer all questions when compared with the Traditional Model Group (224.53 ± 44.13 s vs. 238.71 ± 68.46 s, p = 0.09), but the total score was not significantly different (6.24 ± 1.30 vs. 7.18 ± 1.70, p = 0.12). Neither the students'satisfaction (p = 0.48) nor their understanding of cardiac structures (p = 0.24) was significantly different between two groups. More students in the 3D Printing Group believed that they had understood at least 90% of teaching content (6 vs. 1). Both groups had 12 (70.6%) students who preferred a 3D printing model for medical education. A 3D printing model was not significantly superior to a traditional model in teaching cardiac diseases in our pilot randomized controlled study, yet more studies may be conducted to validate the real effect of 3D printing on medical education.

Is a Three-Dimensional Printing Model Better Than a Traditional Cardiac Model for Medical Education? A Pilot Randomized Controlled Study

PubMed Central

Wang, Zhongmin; Liu, Yuhao; Luo, Hongxing; Gao, Chuanyu; Zhang, Jing; Dai, Yuya

2017-01-01

Background Three-dimensional (3D) printing is a newly-emerged technology converting a series of two-dimensional images to a touchable 3D model, but no studies have investigated whether or not a 3D printing model is better than a traditional cardiac model for medical education. Methods A 3D printing cardiac model was generated using multi-slice computed tomography datasets. Thirty-four medical students were randomized to either the 3D Printing Group taught with the aid of a 3D printing cardiac model or the Traditional Model Group with a commonly used plastic cardiac model. Questionnaires with 10 medical questions and 3 evaluative questions were filled in by the students. Results A 3D printing cardiac model was successfully generated. Students in the 3D Printing Group were slightly quicker to answer all questions when compared with the Traditional Model Group (224.53 ± 44.13 s vs. 238.71 ± 68.46 s, p = 0.09), but the total score was not significantly different (6.24 ± 1.30 vs. 7.18 ± 1.70, p = 0.12). Neither the students’satisfaction (p = 0.48) nor their understanding of cardiac structures (p = 0.24) was significantly different between two groups. More students in the 3D Printing Group believed that they had understood at least 90% of teaching content (6 vs. 1). Both groups had 12 (70.6%) students who preferred a 3D printing model for medical education. Conclusions A 3D printing model was not significantly superior to a traditional model in teaching cardiac diseases in our pilot randomized controlled study, yet more studies may be conducted to validate the real effect of 3D printing on medical education. PMID:29167621

Geometries of geoelectrical structures in central Tibetan Plateau from INDEPTH magnetotelluric data

NASA Astrophysics Data System (ADS)

Vozar, Jan; Jones, Alan G.; Le Pape, Florian

2013-04-01

Magnetotelluric (MT) data collected on N-S profiles crossing the Banggong-Nujiang Suture, which separates the Qiangtang and Lhasa Terranes in central Tibet, as a part of InterNational DEep Profiling of Tibet and the Himalaya project (INDEPTH) are modeled by 2D and 3D inversion codes. The 2D deep MT model of line 500 confirms previous observations concluding that the region is characterized to first-order by a resistive upper crust and a conductive, partially melted, middle to lower crust that extends from the Lhasa Terrane to the Qiangtang Terrane with varying depth. The same conductive structure setting, but in shallower depths is also present on the eastern 400 line. From deep electromagnetic sounding, supported by independent 1D integrated petro-physical investigation, we can estimate the next upper-mantle conductive layer at depths from 200 km to 250 km below the Lhasa Terrane and less resistive Tibetan lithosphere below the Qiangtang Terrane with conductive upper-mantle in depths about 120 km. The anisotropic 2D modeling reveals lower crustal anisotropy in Lhasa Terrane, which can interpreted as crustal channel flow. The 3D inversion models of all MT data from central Tibet show dominant 2D regional strike of mid and lower crustal structures equal N110E. This orientation is parallel to Shuanghu suture, BengCo Jiali strike-slip fault system and perpendicular to convergence direction. The lower crust conductor in central Lhasa Terrane can be interpreted more likely as 3D lower Indian crust structure, located to the east from line 500, than geoelectrical anisotropic crustal flow.

Quality assessment of protein model-structures based on structural and functional similarities.

PubMed

Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

2012-09-21

Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and one of CASP9, compared to the contest participants. Consequently, GOBA offers a novel single model quality assessment program that addresses the practical needs of biologists. In conjunction with other Model Quality Assessment Programs (MQAPs), it would prove useful for the evaluation of single protein models.

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

PubMed

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

2016-04-20

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

Synthesis of image sequences for Korean sign language using 3D shape model

NASA Astrophysics Data System (ADS)

Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

1995-05-01

This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

Product Line Acquisition in the DoD: The Promise, The Challenges

DTIC Science & Technology

1999-12-01

Organizational Structure 8 3.4 Providing an Appropriate Funding Model 9 3.5 Developing and Implementing an Acquisition Strategy 10 3.6 Contractor Interface...providing an appropriate funding model • achieving the right organizational structure • developing and implementing an acquisition strategy • contractor...organizational change rather than attempt a risky enterprise overhaul. 3.4 Providing an Appropriate Funding Model The funding model is closely

Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics.

PubMed

Kaczor, Agnieszka A; Silva, Andrea G; Loza, María I; Kolb, Peter; Castro, Marián; Poso, Antti

2016-04-05

Structure-based virtual screening using a D2 receptor homology model was performed to identify dopamine D2 receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D2 ligands were identified (47.6% success rate, among them D2 receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5-HT2A receptors. The affinity (Ki values) of the compounds ranged from 58 nm to about 24 μM. Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D2 receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D2 pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20-fold binding selectivity for the D2 receptor over the D3 receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D toroidal physics: testing the boundaries of symmetry breaking

NASA Astrophysics Data System (ADS)

Spong, Don

2014-10-01

Toroidal symmetry is an important concept for plasma confinement; it allows the existence of nested flux surface MHD equilibria and conserved invariants for particle motion. However, perfect symmetry is unachievable in realistic toroidal plasma devices. For example, tokamaks have toroidal ripple due to discrete field coils, optimized stellarators do not achieve exact quasi-symmetry, the plasma itself continually seeks lower energy states through helical 3D deformations, and reactors will likely have non-uniform distributions of ferritic steel near the plasma. Also, some level of designed-in 3D magnetic field structure is now anticipated for most concepts in order to lead to a stable, steady-state fusion reactor. Such planned 3D field structures can take many forms, ranging from tokamaks with weak 3D ELM-suppression fields to stellarators with more dominant 3D field structures. There is considerable interest in the development of unified physics models for the full range of 3D effects. Ultimately, the questions of how much symmetry breaking can be tolerated and how to optimize its design must be addressed for all fusion concepts. Fortunately, significant progress is underway in theory, computation and plasma diagnostics on many issues such as magnetic surface quality, plasma screening vs. amplification of 3D perturbations, 3D transport, influence on edge pedestal structures, MHD stability effects, modification of fast ion-driven instabilities, prediction of energetic particle heat loads on plasma-facing materials, effects of 3D fields on turbulence, and magnetic coil design. A closely coupled program of simulation, experimental validation, and design optimization is required to determine what forms and amplitudes of 3D shaping and symmetry breaking will be compatible with future fusion reactors. The development of models to address 3D physics and progress in these areas will be described. This work is supported both by the US Department of Energy under Contract DE-AC05-00OR22725 with UT-Battelle, LLC and under the US DOE SciDAC GSEP Center.

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

NASA Astrophysics Data System (ADS)

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

1998-06-01

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

FUN3D and CFL3D Computations for the First High Lift Prediction Workshop

NASA Technical Reports Server (NTRS)

Park, Michael A.; Lee-Rausch, Elizabeth M.; Rumsey, Christopher L.

2011-01-01

Two Reynolds-averaged Navier-Stokes codes were used to compute flow over the NASA Trapezoidal Wing at high lift conditions for the 1st AIAA CFD High Lift Prediction Workshop, held in Chicago in June 2010. The unstructured-grid code FUN3D and the structured-grid code CFL3D were applied to several different grid systems. The effects of code, grid system, turbulence model, viscous term treatment, and brackets were studied. The SST model on this configuration predicted lower lift than the Spalart-Allmaras model at high angles of attack; the Spalart-Allmaras model agreed better with experiment. Neglecting viscous cross-derivative terms caused poorer prediction in the wing tip vortex region. Output-based grid adaptation was applied to the unstructured-grid solutions. The adapted grids better resolved wake structures and reduced flap flow separation, which was also observed in uniform grid refinement studies. Limitations of the adaptation method as well as areas for future improvement were identified.

3D-quantitative structure-activity relationship studies on benzothiadiazepine hydroxamates as inhibitors of tumor necrosis factor-alpha converting enzyme.

PubMed

Murumkar, Prashant R; Giridhar, Rajani; Yadav, Mange Ram

2008-04-01

A set of 29 benzothiadiazepine hydroxamates having selective tumor necrosis factor-alpha converting enzyme inhibitory activity were used to compare the quality and predictive power of 3D-quantitative structure-activity relationship, comparative molecular field analysis, and comparative molecular similarity indices models for the atom-based, centroid/atom-based, data-based, and docked conformer-based alignment. Removal of two outliers from the initial training set of molecules improved the predictivity of models. Among the 3D-quantitative structure-activity relationship models developed using the above four alignments, the database alignment provided the optimal predictive comparative molecular field analysis model for the training set with cross-validated r(2) (q(2)) = 0.510, non-cross-validated r(2) = 0.972, standard error of estimates (s) = 0.098, and F = 215.44 and the optimal comparative molecular similarity indices model with cross-validated r(2) (q(2)) = 0.556, non-cross-validated r(2) = 0.946, standard error of estimates (s) = 0.163, and F = 99.785. These models also showed the best test set prediction for six compounds with predictive r(2) values of 0.460 and 0.535, respectively. The contour maps obtained from 3D-quantitative structure-activity relationship studies were appraised for activity trends for the molecules analyzed. The comparative molecular similarity indices models exhibited good external predictivity as compared with that of comparative molecular field analysis models. The data generated from the present study helped us to further design and report some novel and potent tumor necrosis factor-alpha converting enzyme inhibitors.

Three-dimensional reconstruction of coronary arteries and its application in localization of coronary artery segments corresponding to myocardial segments identified by transthoracic echocardiography.

PubMed

Zhong, Chunyan; Guo, Yanli; Huang, Haiyun; Tan, Liwen; Wu, Yi; Wang, Wenting

2013-01-01

To establish 3D models of coronary arteries (CA) and study their application in localization of CA segments identified by Transthoracic Echocardiography (TTE). Sectional images of the heart collected from the first CVH dataset and contrast CT data were used to establish 3D models of the CA. Virtual dissection was performed on the 3D models to simulate the conventional sections of TTE. Then, we used 2D ultrasound, speckle tracking imaging (STI), and 2D ultrasound plus 3D CA models to diagnose 170 patients and compare the results to coronary angiography (CAG). 3D models of CA distinctly displayed both 3D structure and 2D sections of CA. This simulated TTE imaging in any plane and showed the CA segments that corresponded to 17 myocardial segments identified by TTE. The localization accuracy showed a significant difference between 2D ultrasound and 2D ultrasound plus 3D CA model in the severe stenosis group (P < 0.05) and in the mild-to-moderate stenosis group (P < 0.05). These innovative modeling techniques help clinicians identify the CA segments that correspond to myocardial segments typically shown in TTE sectional images, thereby increasing the accuracy of the TTE-based diagnosis of CHD.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Studies of New Fused Benzazepine as Selective Dopamine D3 Receptor Antagonists Using 3D-QSAR, Molecular Docking and Molecular Dynamics

PubMed Central

Liu, Jing; Li, Yan; Zhang, Shuwei; Xiao, Zhengtao; Ai, Chunzhi

2011-01-01

In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q2 = 0.603, R2ncv = 0.829, R2pre = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q2 = 0.506, R2ncv =0.838, R2pre = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R3 substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R1 substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists. PMID:21541053

Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics.

PubMed

Liu, Jing; Li, Yan; Zhang, Shuwei; Xiao, Zhengtao; Ai, Chunzhi

2011-02-18

In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q(2) = 0.603, R(2) (ncv) = 0.829, R(2) (pre) = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q(2) = 0.506, R(2) (ncv) =0.838, R(2) (pre) = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R(3) substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R(1) substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists.

"Let's get physical": advantages of a physical model over 3D computer models and textbooks in learning imaging anatomy.

PubMed

Preece, Daniel; Williams, Sarah B; Lam, Richard; Weller, Renate

2013-01-01

Three-dimensional (3D) information plays an important part in medical and veterinary education. Appreciating complex 3D spatial relationships requires a strong foundational understanding of anatomy and mental 3D visualization skills. Novel learning resources have been introduced to anatomy training to achieve this. Objective evaluation of their comparative efficacies remains scarce in the literature. This study developed and evaluated the use of a physical model in demonstrating the complex spatial relationships of the equine foot. It was hypothesized that the newly developed physical model would be more effective for students to learn magnetic resonance imaging (MRI) anatomy of the foot than textbooks or computer-based 3D models. Third year veterinary medicine students were randomly assigned to one of three teaching aid groups (physical model; textbooks; 3D computer model). The comparative efficacies of the three teaching aids were assessed through students' abilities to identify anatomical structures on MR images. Overall mean MRI assessment scores were significantly higher in students utilizing the physical model (86.39%) compared with students using textbooks (62.61%) and the 3D computer model (63.68%) (P < 0.001), with no significant difference between the textbook and 3D computer model groups (P = 0.685). Student feedback was also more positive in the physical model group compared with both the textbook and 3D computer model groups. Our results suggest that physical models may hold a significant advantage over alternative learning resources in enhancing visuospatial and 3D understanding of complex anatomical architecture, and that 3D computer models have significant limitations with regards to 3D learning. © 2013 American Association of Anatomists.

3D reconstruction of SEM images by use of optical photogrammetry software.

PubMed

Eulitz, Mona; Reiss, Gebhard

2015-08-01

Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching. Copyright © 2015 Elsevier Inc. All rights reserved.

Realistic 3D computer model of the gerbil middle ear, featuring accurate morphology of bone and soft tissue structures.

PubMed

Buytaert, Jan A N; Salih, Wasil H M; Dierick, Manual; Jacobs, Patric; Dirckx, Joris J J

2011-12-01

In order to improve realism in middle ear (ME) finite-element modeling (FEM), comprehensive and precise morphological data are needed. To date, micro-scale X-ray computed tomography (μCT) recordings have been used as geometric input data for FEM models of the ME ossicles. Previously, attempts were made to obtain these data on ME soft tissue structures as well. However, due to low X-ray absorption of soft tissue, quality of these images is limited. Another popular approach is using histological sections as data for 3D models, delivering high in-plane resolution for the sections, but the technique is destructive in nature and registration of the sections is difficult. We combine data from high-resolution μCT recordings with data from high-resolution orthogonal-plane fluorescence optical-sectioning microscopy (OPFOS), both obtained on the same gerbil specimen. State-of-the-art μCT delivers high-resolution data on the 3D shape of ossicles and other ME bony structures, while the OPFOS setup generates data of unprecedented quality both on bone and soft tissue ME structures. Each of these techniques is tomographic and non-destructive and delivers sets of automatically aligned virtual sections. The datasets coming from different techniques need to be registered with respect to each other. By combining both datasets, we obtain a complete high-resolution morphological model of all functional components in the gerbil ME. The resulting 3D model can be readily imported in FEM software and is made freely available to the research community. In this paper, we discuss the methods used, present the resulting merged model, and discuss the morphological properties of the soft tissue structures, such as muscles and ligaments.

3D electromagnetic modelling of a TTI medium and TTI effects in inversion

NASA Astrophysics Data System (ADS)

Jaysaval, Piyoosh; Shantsev, Daniil; de la Kethulle de Ryhove, Sébastien

2016-04-01

We present a numerical algorithm for 3D electromagnetic (EM) forward modelling in conducting media with general electric anisotropy. The algorithm is based on the finite-difference discretization of frequency-domain Maxwell's equations on a Lebedev grid, in which all components of the electric field are collocated but half a spatial step staggered with respect to the magnetic field components, which also are collocated. This leads to a system of linear equations that is solved using a stabilized biconjugate gradient method with a multigrid preconditioner. We validate the accuracy of the numerical results for layered and 3D tilted transverse isotropic (TTI) earth models representing typical scenarios used in the marine controlled-source EM method. It is then demonstrated that not taking into account the full anisotropy of the conductivity tensor can lead to misleading inversion results. For simulation data corresponding to a 3D model with a TTI anticlinal structure, a standard vertical transverse isotropic inversion is not able to image a resistor, while for a 3D model with a TTI synclinal structure the inversion produces a false resistive anomaly. If inversion uses the proposed forward solver that can handle TTI anisotropy, it produces resistivity images consistent with the true models.

Tactical 3D Model Generation using Structure-From-Motion on Video from Unmanned Systems

DTIC Science & Technology

2015-04-01

available SfM application known as VisualSFM .6,7 VisualSFM is an end-user, “off-the-shelf” implementation of SfM that is easy to configure and used for...most 3D model generation applications from imagery. While the usual interface with VisualSFM is through their graphical user interface (GUI), we will be...of our system.5 There are two types of 3D model generation available within VisualSFM ; sparse and dense reconstruction. Sparse reconstruction begins

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.

Rigorous joining of advanced reduced-dimensional beam models to three-dimensional finite element models

NASA Astrophysics Data System (ADS)

Song, Huimin

In the aerospace and automotive industries, many finite element analyses use lower-dimensional finite elements such as beams, plates and shells, to simplify the modeling. These simplified models can greatly reduce the computation time and cost; however, reduced-dimensional models may introduce inaccuracies, particularly near boundaries and near portions of the structure where reduced-dimensional models may not apply. Another factor in creation of such models is that beam-like structures frequently have complex geometry, boundaries and loading conditions, which may make them unsuitable for modeling with single type of element. The goal of this dissertation is to develop a method that can accurately and efficiently capture the response of a structure by rigorous combination of a reduced-dimensional beam finite element model with a model based on full two-dimensional (2D) or three-dimensional (3D) finite elements. The first chapter of the thesis gives the background of the present work and some related previous work. The second chapter is focused on formulating a system of equations that govern the joining of a 2D model with a beam model for planar deformation. The essential aspect of this formulation is to find the transformation matrices to achieve deflection and load continuity on the interface. Three approaches are provided to obtain the transformation matrices. An example based on joining a beam to a 2D finite element model is examined, and the accuracy of the analysis is studied by comparing joint results with the full 2D analysis. The third chapter is focused on formulating the system of equations for joining a beam to a 3D finite element model for static and free-vibration problems. The transition between the 3D elements and beam elements is achieved by use of the stress recovery technique of the variational-asymptotic method as implemented in VABS (the Variational Asymptotic Beam Section analysis). The formulations for an interface transformation matrix and the generalized Timoshenko beam are discussed in this chapter. VABS is also used to obtain the beam constitutive properties and warping functions for stress recovery. Several 3D-beam joint examples are presented to show the convergence and accuracy of the analysis. Accuracy is accessed by comparing the joint results with the full 3D analysis. The fourth chapter provides conclusions from present studies and recommendations for future work.

3D Laser Imprint Using a Smoother Ray-Traced Power Deposition Method

NASA Astrophysics Data System (ADS)

Schmitt, Andrew J.

2017-10-01

Imprinting of laser nonuniformities in directly-driven icf targets is a challenging problem to accurately simulate with large radiation-hydro codes. One of the most challenging aspects is the proper construction of the complex and rapidly changing laser interference structure driving the imprint using the reduced laser propagation models (usually ray-tracing) found in these codes. We have upgraded the modelling capability in our massively-parallel fastrad3d code by adding a more realistic EM-wave interference structure. This interference model adds an axial laser speckle to the previous transverse-only laser structure, and can be impressed on our improved smoothed 3D raytrace package. This latter package, which connects rays to form bundles and performs power deposition calculations on the bundles, is intended to decrease ray-trace noise (which can mask or add to imprint) while using fewer rays. We apply this improved model to 3D simulations of recent imprint experiments performed on the Omega-EP laser and the Nike laser that examined the reduction of imprinting due to very thin high-Z target coatings. We report on the conditions in which this new model makes a significant impact on the development of laser imprint. Supported by US DoE/NNSA.

3D numerical modelling of negative apparent conductivity anomalies in loop-loop electromagnetic measurements: a case study at a dacite intrusion in Sugisawa, Akita Prefecture, Japan

NASA Astrophysics Data System (ADS)

Selepeng, Ame Thato; Sakanaka, Shin'ya; Nishitani, Tadashi

2017-04-01

Under certain geological conditions, low induction number electromagnetic (LIN-EM) instruments are known to produce negative apparent conductivity (σa) responses. This is particularly the case when the shallow subsurface is characterised by highly conductive bodies, however little attention has been given to this issue in the research literature. To analyse negative σa anomalies and their causative structures, we make use of a 3D integral equation forward modelling technique based on a 3D weighting function. We present 3D numerical modelling results over a volcanic tuff body intruded by several dacite dikes, in Sugisawa, Akita Prefecture, Japan. Apparent conductivity data were acquired using a Geonics EM-34-3 system in the horizontal magnetic dipole (HMD) and vertical magnetic dipole (VMD) operating modes. Our 3D model resolved the horizontal and vertical extent of the dacite dikes and also delineated a high conductive zone between the volcanic tuff and the intrusive dacite dikes. This zone is the causative structure for negative σa responses in the VMD data, and is interpreted to be an alteration zone. Interestingly, the negative σa response was absent when the instrument alignment azimuth was changed, implying an anisotropic effect on the EM signature in the study area. The true conductivity model achieved by 3D forward modelling is shown to compare favourably with the DC resistivity data acquired in the same area.

RAPID COMMUNICATION: Study of superstructure II in multiferroic BiMnO3

NASA Astrophysics Data System (ADS)

Ge, Bing-Hui; Li, Fang-Hua; Li, Xue-Ming; Wang, Yu-Mei; Chi, Zhen-Hua; Jin, Chang-Qing

2008-09-01

The crystal structure of the minor phase, named superstructure II, existing in multiferroic compound BiMnO3 has been studied by electron diffraction and high-resolution transmission electron microscopy. Domains of major and minor phases coexisting in BiMnO3 were observed in high-resolution electron microscope images. The unit cell of minor phase was determined to be triclinic with the size 4×4×4 times as large as the distorted perovskite subcell. The [111] and [10bar 1] projected structure maps of the minor phase have been derived from the corresponding images by means of the image processing. A possible rough three-dimensional (3D) structure model was proposed based on the 3D structural information extracted from the two projected structure maps. Since there is no inversion centre in the proposed model, the minor phase may contribute to the ferroelectric property of BiMnO3.

Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-Chromen-2-One Core: Structure-Based and Ligand-Based Derived Three-Dimensional Quantitative Structure-Activity Relationships Predictive Models.

PubMed

Mladenović, Milan; Patsilinakos, Alexandros; Pirolli, Adele; Sabatino, Manuela; Ragno, Rino

2017-04-24

Monoamine oxidase B (MAO B) catalyzes the oxidative deamination of aryalkylamines neurotransmitters with concomitant reduction of oxygen to hydrogen peroxide. Consequently, the enzyme's malfunction can induce oxidative damage to mitochondrial DNA and mediates development of Parkinson's disease. Thus, MAO B emerges as a promising target for developing pharmaceuticals potentially useful to treat this vicious neurodegenerative condition. Aiming to contribute to the development of drugs with the reversible mechanism of MAO B inhibition only, herein, an extended in silico-in vitro procedure for the selection of novel MAO B inhibitors is demonstrated, including the following: (1) definition of optimized and validated structure-based three-dimensional (3-D) quantitative structure-activity relationships (QSAR) models derived from available cocrystallized inhibitor-MAO B complexes; (2) elaboration of SAR features for either irreversible or reversible MAO B inhibitors to characterize and improve coumarin-based inhibitor activity (Protein Data Bank ID: 2V61 ) as the most potent reversible lead compound; (3) definition of structure-based (SB) and ligand-based (LB) alignment rule assessments by which virtually any untested potential MAO B inhibitor might be evaluated; (4) predictive ability validation of the best 3-D QSAR model through SB/LB modeling of four coumarin-based external test sets (267 compounds); (5) design and SB/LB alignment of novel coumarin-based scaffolds experimentally validated through synthesis and biological evaluation in vitro. Due to the wide range of molecular diversity within the 3-D QSAR training set and derived features, the selected N probe-derived 3-D QSAR model proves to be a valuable tool for virtual screening (VS) of novel MAO B inhibitors and a platform for design, synthesis and evaluation of novel active structures. Accordingly, six highly active and selective MAO B inhibitors (picomolar to low nanomolar range of activity) were disclosed as a result of rational SB/LB 3D QSAR design; therefore, D123 (IC 50 = 0.83 nM, K i = 0.25 nM) and D124 (IC 50 = 0.97 nM, K i = 0.29 nM) are potential lead candidates as anti-Parkinson's drugs.

3D RNA and functional interactions from evolutionary couplings

PubMed Central

Weinreb, Caleb; Riesselman, Adam; Ingraham, John B.; Gross, Torsten; Sander, Chris; Marks, Debora S.

2016-01-01

Summary Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules, and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions, e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by accelerating sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA. PMID:27087444

Benchmarking an Unstructured-Grid Model for Tsunami Current Modeling

NASA Astrophysics Data System (ADS)

Zhang, Yinglong J.; Priest, George; Allan, Jonathan; Stimely, Laura

2016-12-01

We present model results derived from a tsunami current benchmarking workshop held by the NTHMP (National Tsunami Hazard Mitigation Program) in February 2015. Modeling was undertaken using our own 3D unstructured-grid model that has been previously certified by the NTHMP for tsunami inundation. Results for two benchmark tests are described here, including: (1) vortex structure in the wake of a submerged shoal and (2) impact of tsunami waves on Hilo Harbor in the 2011 Tohoku event. The modeled current velocities are compared with available lab and field data. We demonstrate that the model is able to accurately capture the velocity field in the two benchmark tests; in particular, the 3D model gives a much more accurate wake structure than the 2D model for the first test, with the root-mean-square error and mean bias no more than 2 cm s-1 and 8 mm s-1, respectively, for the modeled velocity.

An automated method for modeling proteins on known templates using distance geometry.

PubMed

Srinivasan, S; March, C J; Sudarsanam, S

1993-02-01

We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. Starting with the sequence alignment of a family of homologous proteins, tertiary structures are modeled using the known 3D structure of one member of the family as a template. Homologous interatomic distances from the template are used as constraints. For nonhomologous regions in the model protein, the lower and the upper bounds for the interatomic distances are imposed by steric constraints and the globular dimensions of the template, respectively. Distance geometry is used to embed an ensemble of structures consistent with these distance bounds. Structures are selected from this ensemble based on minimal distance error criteria, after a penalty function optimization step. These structures are then refined using energy optimization methods. The method is tested by simulating the alpha-chain of horse hemoglobin using the alpha-chain of human hemoglobin as the template and by comparing the generated models with the crystal structure of the alpha-chain of horse hemoglobin. We also test the packing efficiency of this method by reconstructing the atomic positions of the interior side chains beyond C beta atoms of a protein domain from a known 3D structure. In both test cases, models retain the template constraints and any additionally imposed constraints while the packing of the interior residues is optimized with no short contacts or bond deformations. To demonstrate the use of this method in simulating structures of proteins with nonhomologous disulfides, we construct a model of murine interleukin (IL)-4 using the NMR structure of human IL-4 as the template. The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry.

A Prototype Educational Model for Hepatobiliary Interventions: Unveiling the Role of Graphic Designers in Medical 3D Printing.

PubMed

Javan, Ramin; Zeman, Merissa N

2018-02-01

In the context of medical three-dimensional (3D) printing, in addition to 3D reconstruction from cross-sectional imaging, graphic design plays a role in developing and/or enhancing 3D-printed models. A custom prototype modular 3D model of the liver was graphically designed depicting segmental anatomy of the parenchyma containing color-coded hepatic vasculature and biliary tree. Subsequently, 3D printing was performed using transparent resin for the surface of the liver and polyamide material to develop hollow internal structures that allow for passage of catheters and wires. A number of concepts were incorporated into the model. A representative mass with surrounding feeding arterial supply was embedded to demonstrate tumor embolization. A straight narrow hollow tract connecting the mass to the surface of the liver, displaying the path of a biopsy device's needle, and the concept of needle "throw" length was designed. A connection between the middle hepatic and right portal veins was created to demonstrate transjugular intrahepatic portosystemic shunt (TIPS) placement. A hollow amorphous structure representing an abscess was created to allow the demonstration of drainage catheter placement with the formation of pigtail tip. Percutaneous biliary drain and cholecystostomy tube placement were also represented. The skills of graphic designers may be utilized in creating highly customized 3D-printed models. A model was developed for the demonstration and simulation of multiple hepatobiliary interventions, for training purposes, patient counseling and consenting, and as a prototype for future development of a functioning interventional phantom.

Deconstructing three-dimensional (3D) structure of absorptive glass mat (AGM) separator to tailor pore dimensions and amplify electrolyte uptake

NASA Astrophysics Data System (ADS)

Rawal, Amit; Rao, P. V. Kameswara; Kumar, Vijay

2018-04-01

Absorptive glass mat (AGM) separator is a vital technical component in valve regulated lead acid (VRLA) batteries that can be tailored for a desired application. To selectively design and tailor the AGM separator, the intricate three-dimensional (3D) structure needs to be unraveled. Herein, a toolkit of 3D analytical models of pore size distribution and electrolyte uptake expressed via wicking characteristics of AGM separators under unconfined and confined states is presented. 3D data of fiber orientation distributions obtained previously through X-ray micro-computed tomography (microCT) analysis are used as key set of input parameters. The predictive ability of pore size distribution model is assessed through the commonly used experimental set-up that usually apply high level of compressive stresses. Further, the existing analytical model of wicking characteristics of AGM separators has been extended to account for 3D characteristics, and subsequently, compared with the experimental results. A good agreement between the theory and experiments pave the way to simulate the realistic charge-discharge modes of the battery by applying cyclic loading condition. A threshold criterion describing the invariant behavior of pore size and wicking characteristics in terms of maximum permissible limit of key structural parameters during charge-discharge mode of the battery has also been proposed.

Integration of multi-source and multi-scale datasets for 3D structural modeling for subsurface exploration targeting, Luanchuan Mo-polymetallic district, China

NASA Astrophysics Data System (ADS)

Wang, Gongwen; Ma, Zhenbo; Li, Ruixi; Song, Yaowu; Qu, Jianan; Zhang, Shouting; Yan, Changhai; Han, Jiangwei

2017-04-01

In this paper, multi-source (geophysical, geochemical, geological and remote sensing) datasets were used to construct multi-scale (district-, deposit-, and orebody-scale) 3D geological models and extract 3D exploration criteria for subsurface Mo-polymetallic exploration targeting in the Luanchuan district in China. The results indicate that (i) a series of region-/district-scale NW-trending thrusts controlled main Mo-polymetallic forming, and they were formed by regional Indosinian Qinling orogenic events, the secondary NW-trending district-scale folds and NE-trending faults and the intrusive stock structure are produced based on thrust structure in Caledonian-Indosinian orogenic events; they are ore-bearing zones and ore-forming structures; (ii) the NW-trending district-scale and NE-trending deposit-scale normal faults were crossed and controlled by the Jurassic granite stocks in 3D space, they are associated with the magma-skarn Mo polymetallic mineralization (the 3D buffer distance of ore-forming granite stocks is 600 m) and the NW-trending hydrothermal Pb-Zn deposits which are surrounded by the Jurassic granite stocks and constrained by NW-trending or NE-trending faults (the 3D buffer distance of ore-forming fault is 700 m); and (iii) nine Mo polymetallic and four Pb-Zn targets were identified in the subsurface of the Luanchuan district.

Static Aeroelastic Analysis with an Inviscid Cartesian Method

NASA Technical Reports Server (NTRS)

Rodriguez, David L.; Aftosmis, Michael J.; Nemec, Marian; Smith, Stephen C.

2014-01-01

An embedded-boundary Cartesian-mesh flow solver is coupled with a three degree-offreedom structural model to perform static, aeroelastic analysis of complex aircraft geometries. The approach solves the complete system of aero-structural equations using a modular, loosely-coupled strategy which allows the lower-fidelity structural model to deform the highfidelity CFD model. The approach uses an open-source, 3-D discrete-geometry engine to deform a triangulated surface geometry according to the shape predicted by the structural model under the computed aerodynamic loads. The deformation scheme is capable of modeling large deflections and is applicable to the design of modern, very-flexible transport wings. The interface is modular so that aerodynamic or structural analysis methods can be easily swapped or enhanced. This extended abstract includes a brief description of the architecture, along with some preliminary validation of underlying assumptions and early results on a generic 3D transport model. The final paper will present more concrete cases and validation of the approach. Preliminary results demonstrate convergence of the complete aero-structural system and investigate the accuracy of the approximations used in the formulation of the structural model.

A Novel and Freely Available Interactive 3d Model of the Internal Carotid Artery.

PubMed

Valera-Melé, Marc; Puigdellívol-Sánchez, Anna; Mavar-Haramija, Marija; Juanes-Méndez, Juan A; San-Román, Luis; de Notaris, Matteo; Prats-Galino, Alberto

2018-03-05

We describe a new and freely available 3D interactive model of the intracranial internal carotid artery (ICA) and the skull base that also allows to display and compare its main segment classifications. High-resolution 3D human angiography (isometric voxel's size 0.36 mm) and Computed Tomography angiography images were exported to Virtual Reality Modeling Language (VRML) format for processing in a 3D software platform and embedding in a 3D Portable Document Format (PDF) document that can be freely downloaded at http://diposit.ub.edu/dspace/handle/2445/112442 and runs under Acrobat Reader on Mac and Windows computers and Windows 10 tablets. The 3D-PDF allows for visualisation and interaction through JavaScript-based functions (including zoom, rotation, selective visualization and transparentation of structures or a predefined sequence view of the main segment classifications if desired). The ICA and its main branches and loops, the Gasserian ganglion, the petrolingual ligament and the proximal and distal dural rings within the skull base environment (anterior and posterior clinoid processes, silla turcica, ethmoid and sphenoid bones, orbital fossae) may be visualized from different perspectives. This interactive 3D-PDF provides virtual views of the ICA and becomes an innovative tool to improve the understanding of the neuroanatomy of the ICA and surrounding structures.

Do 3D Printing Models Improve Anatomical Teaching About Hepatic Segments to Medical Students? A Randomized Controlled Study.

PubMed

Kong, Xiangxue; Nie, Lanying; Zhang, Huijian; Wang, Zhanglin; Ye, Qiang; Tang, Lei; Huang, Wenhua; Li, Jianyi

2016-08-01

It is a difficult and frustrating task for young surgeons and medical students to understand the anatomy of hepatic segments. We tried to develop an optimal 3D printing model of hepatic segments as a teaching aid to improve the teaching of hepatic segments. A fresh human cadaveric liver without hepatic disease was CT scanned. After 3D reconstruction, three types of 3D computer models of hepatic structures were designed and 3D printed as models of hepatic segments without parenchyma (type 1) and with transparent parenchyma (type 2), and hepatic ducts with segmental partitions (type 3). These models were evaluated by six experts using a five-point Likert scale. Ninety two medical freshmen were randomized into four groups to learn hepatic segments with the aid of the three types of models and traditional anatomic atlas (TAA). Their results of two quizzes were compared to evaluate the teaching effects of the four methods. Three types of models were successful produced which displayed the structures of hepatic segments. By experts' evaluation, type 3 model was better than type 1 and 2 models in anatomical condition, type 2 and 3 models were better than type 1 model in tactility, and type 3 model was better than type 1 model in overall satisfaction (P < 0.05). The first quiz revealed that type 1 model was better than type 2 model and TAA, while type 3 model was better than type 2 and TAA in teaching effects (P < 0.05). The second quiz found that type 1 model was better than TAA, while type 3 model was better than type 2 model and TAA regarding teaching effects (P < 0.05). Only TAA group had significant declines between two quizzes (P < 0.05). The model with segmental partitions proves to be optimal, because it can best improve anatomical teaching about hepatic segments.

Building continental-scale 3D subsurface layers in the Digital Crust project: constrained interpolation and uncertainty estimation.

NASA Astrophysics Data System (ADS)

Yulaeva, E.; Fan, Y.; Moosdorf, N.; Richard, S. M.; Bristol, S.; Peters, S. E.; Zaslavsky, I.; Ingebritsen, S.

2015-12-01

The Digital Crust EarthCube building block creates a framework for integrating disparate 3D/4D information from multiple sources into a comprehensive model of the structure and composition of the Earth's upper crust, and to demonstrate the utility of this model in several research scenarios. One of such scenarios is estimation of various crustal properties related to fluid dynamics (e.g. permeability and porosity) at each node of any arbitrary unstructured 3D grid to support continental-scale numerical models of fluid flow and transport. Starting from Macrostrat, an existing 4D database of 33,903 chronostratigraphic units, and employing GeoDeepDive, a software system for extracting structured information from unstructured documents, we construct 3D gridded fields of sediment/rock porosity, permeability and geochemistry for large sedimentary basins of North America, which will be used to improve our understanding of large-scale fluid flow, chemical weathering rates, and geochemical fluxes into the ocean. In this talk, we discuss the methods, data gaps (particularly in geologically complex terrain), and various physical and geological constraints on interpolation and uncertainty estimation.

Development and assessment of a new 3D neuroanatomy teaching tool for MRI training.

PubMed

Drapkin, Zachary A; Lindgren, Kristen A; Lopez, Michael J; Stabio, Maureen E

2015-01-01

A computerized three-dimensional (3D) neuroanatomy teaching tool was developed for training medical students to identify subcortical structures on a magnetic resonance imaging (MRI) series of the human brain. This program allows the user to transition rapidly between two-dimensional (2D) MRI slices, 3D object composites, and a combined model in which 3D objects are overlaid onto the 2D MRI slices, all while rotating the brain in any direction and advancing through coronal, sagittal, or axial planes. The efficacy of this tool was assessed by comparing scores from an MRI identification quiz and survey in two groups of first-year medical students. The first group was taught using this new 3D teaching tool, and the second group was taught the same content for the same amount of time but with traditional methods, including 2D images of brain MRI slices and 3D models from widely used textbooks and online sources. Students from the experimental group performed marginally better than the control group on overall test score (P = 0.07) and significantly better on test scores extracted from questions involving C-shaped internal brain structures (P < 0.01). Experimental participants also expressed higher confidence in their abilities to visualize the 3D structure of the brain (P = 0.02) after using this tool. Furthermore, when surveyed, 100% of the students in the experimental group recommended this tool for future students. These results suggest that this neuroanatomy teaching tool is an effective way to train medical students to read an MRI of the brain and is particularly effective for teaching C-shaped internal brain structures. © 2015 American Association of Anatomists.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

PubMed Central

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

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

A Head in Virtual Reality: Development of A Dynamic Head and Neck Model

ERIC Educational Resources Information Center

Nguyen, Ngan; Wilson, Timothy D.

2009-01-01

Advances in computer and interface technologies have made it possible to create three-dimensional (3D) computerized models of anatomical structures for visualization, manipulation, and interaction in a virtual 3D environment. In the past few decades, a multitude of digital models have been developed to facilitate complex spatial learning of the…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodgers, Arthur J.; Dreger, Douglas S.; Pitarka, Arben

We performed three-dimensional (3D) anelastic ground motion simulations of the South Napa earthquake to investigate the performance of different finite rupture models and the effects of 3D structure on the observed wavefield. We considered rupture models reported by Dreger et al. (2015), Ji et al., (2015), Wei et al. (2015) and Melgar et al. (2015). We used the SW4 anelastic finite difference code developed at Lawrence Livermore National Laboratory (Petersson and Sjogreen, 2013) and distributed by the Computational Infrastructure for Geodynamics. This code can compute the seismic response for fully 3D sub-surface models, including surface topography and linear anelasticity. Wemore » use the 3D geologic/seismic model of the San Francisco Bay Area developed by the United States Geological Survey (Aagaard et al., 2008, 2010). Evaluation of earlier versions of this model indicated that the structure can reproduce main features of observed waveforms from moderate earthquakes (Rodgers et al., 2008; Kim et al., 2010). Simulations were performed for a domain covering local distances (< 25 km) and resolution providing simulated ground motions valid to 1 Hz.« less

Adjoint tomography of Europe

NASA Astrophysics Data System (ADS)

Zhu, H.; Bozdag, E.; Peter, D. B.; Tromp, J.

2010-12-01

We use spectral-element and adjoint methods to image crustal and upper mantle heterogeneity in Europe. The study area involves the convergent boundaries of the Eurasian, African and Arabian plates and the divergent boundary between the Eurasian and North American plates, making the tectonic structure of this region complex. Our goal is to iteratively fit observed seismograms and improve crustal and upper mantle images by taking advantage of 3D forward and inverse modeling techniques. We use data from 200 earthquakes with magnitudes between 5 and 6 recorded by 262 stations provided by ORFEUS. Crustal model Crust2.0 combined with mantle model S362ANI comprise the initial 3D model. Before the iterative adjoint inversion, we determine earthquake source parameters in the initial 3D model by using 3D Green functions and their Fréchet derivatives with respect to the source parameters (i.e., centroid moment tensor and location). The updated catalog is used in the subsequent structural inversion. Since we concentrate on upper mantle structures which involve anisotropy, transversely isotropic (frequency-dependent) traveltime sensitivity kernels are used in the iterative inversion. Taking advantage of the adjoint method, we use as many measurements as can obtain based on comparisons between observed and synthetic seismograms. FLEXWIN (Maggi et al., 2009) is used to automatically select measurement windows which are analyzed based on a multitaper technique. The bandpass ranges from 15 second to 150 second. Long-period surface waves and short-period body waves are combined in source relocations and structural inversions. A statistical assessments of traveltime anomalies and logarithmic waveform differences is used to characterize the inverted sources and structure.

Performance of linear and nonlinear texture measures in 2D and 3D for monitoring architectural changes in osteoporosis using computer-generated models of trabecular bone

NASA Astrophysics Data System (ADS)

Boehm, Holger F.; Link, Thomas M.; Monetti, Roberto A.; Mueller, Dirk; Rummeny, Ernst J.; Raeth, Christoph W.

2005-04-01

Osteoporosis is a metabolic bone disease leading to de-mineralization and increased risk of fracture. The two major factors that determine the biomechanical competence of bone are the degree of mineralization and the micro-architectural integrity. Today, modern imaging modalities (high resolution MRI, micro-CT) are capable of depicting structural details of trabecular bone tissue. From the image data, structural properties obtained by quantitative measures are analysed with respect to the presence of osteoporotic fractures of the spine (in-vivo) or correlated with biomechanical strength as derived from destructive testing (in-vitro). Fairly well established are linear structural measures in 2D that are originally adopted from standard histo-morphometry. Recently, non-linear techniques in 2D and 3D based on the scaling index method (SIM), the standard Hough transform (SHT), and the Minkowski Functionals (MF) have been introduced, which show excellent performance in predicting bone strength and fracture risk. However, little is known about the performance of the various parameters with respect to monitoring structural changes due to progression of osteoporosis or as a result of medical treatment. In this contribution, we generate models of trabecular bone with pre-defined structural properties which are exposed to simulated osteoclastic activity. We apply linear and non-linear texture measures to the models and analyse their performance with respect to detecting architectural changes. This study demonstrates, that the texture measures are capable of monitoring structural changes of complex model data. The diagnostic potential varies for the different parameters and is found to depend on the topological composition of the model and initial "bone density". In our models, non-linear texture measures tend to react more sensitively to small structural changes than linear measures. Best performance is observed for the 3rd and 4th Minkowski Functionals and for the scaling index method.

A 3D Tomographic Model of Asia Based on Pn and P Travel Times from GT Events

NASA Astrophysics Data System (ADS)

Young, C. J.; Begnaud, M. L.; Ballard, S.; Phillips, W. S.; Hipp, J. R.; Steck, L. K.; Rowe, C. A.; Chang, M. C.

2008-12-01

Increasingly, nuclear explosion monitoring is focusing on detection, location, and identification of small events recorded at regional distances. Because Earth structure is highly variable on regional scales, locating events accurately at these distances requires the use of region-specific models to provide accurate travel times. Improved results have been achieved with composites of 1D models and with approximate 3D models with simplified upper mantle structures, but both approaches introduce non-physical boundaries that are problematic for operational monitoring use. Ultimately, what is needed is a true, seamless 3D model of the Earth. Towards that goal, we have developed a 3D tomographic model of the P velocity of the crust and mantle for the Asian continent. Our model is derived by an iterative least squares travel time inversion of more than one million Pn and teleseismic P picks from some 35,000 events recorded at 4,000+ stations. We invert for P velocities from the top of the crust to the core mantle boundary, along with source and receiver static time terms to account for the effects of event mislocation and unaccounted for fine-scale structure near the receiver. Because large portions of the model are under-constrained, we apply spatially varying damping, which constrains the inversion to update the starting model only where good data coverage is available. Our starting crustal model is taken from the a priori crust and upper mantle model of Asia developed through National Nuclear Security Administration laboratory collaboration, which is based on various global and regional studies, and we substantially increase the damping in the crust to discourage changes from this model. Our starting mantle model is AK135. To simplify the inversion, we fix the depths of the major mantle discontinuities (Moho, 410 km, 660 km). 3D rays are calculated using an implementation of the Um and Thurber ray pseudo-bending approach, with full enforcement of Snell's Law in 3D at the major discontinuities. Due to the highly non-linear nature of our ray tracer, we are forced to substantially damp the inversion in order to converge on a reasonable model. We apply both horizontal and vertical regularization to produce smooth models with velocity feature scale lengths that are consistent with established conventions for mantle velocity structure. To investigate the importance of using true 3D rays for the inversion, as opposed to proxy rays through a reference model, we compare our model and ray paths with the model and ray paths resulting from inverting the same data set using rays traced through a 1D reference model. Finally, we validate the model by performing several inversions with random portions of the data set omitted and then testing the predictive capability of the model against those portions compared with AK135. We test the location performance of the model by relocating the GT events using our model and using AK135. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04- 94AL85000.

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

PubMed

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2010-11-01

Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported. Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.

Volumetric visualization of multiple-return LIDAR data: Using voxels

USGS Publications Warehouse

Stoker, Jason M.

2009-01-01

Elevation data are an important component in the visualization and analysis of geographic information. The creation and display of 3D models representing bare earth, vegetation, and surface structures have become a major focus of light detection and ranging (lidar) remote sensing research in the past few years. Lidar is an active sensor that records the distance, or range, of a laser usually fi red from an airplane, helicopter, or satellite. By converting the millions of 3D lidar returns from a system into bare ground, vegetation, or structural elevation information, extremely accurate, high-resolution elevation models can be derived and produced to visualize and quantify scenes in three dimensions. These data can be used to produce high-resolution bare-earth digital elevation models; quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass; and models of urban areas such as building footprints and 3D city models.

The Three-Dimensional Culture System with Matrigel and Neurotrophic Factors Preserves the Structure and Function of Spiral Ganglion Neuron In Vitro.

PubMed

Sun, Gaoying; Liu, Wenwen; Fan, Zhaomin; Zhang, Daogong; Han, Yuechen; Xu, Lei; Qi, Jieyu; Zhang, Shasha; Gao, Bradley T; Bai, Xiaohui; Li, Jianfeng; Chai, Renjie; Wang, Haibo

2016-01-01

Whole organ culture of the spiral ganglion region is a resourceful model system facilitating manipulation and analysis of live sprial ganglion neurons (SGNs). Three-dimensional (3D) cultures have been demonstrated to have many biomedical applications, but the effect of 3D culture in maintaining the SGNs structure and function in explant culture remains uninvestigated. In this study, we used the matrigel to encapsulate the spiral ganglion region isolated from neonatal mice. First, we optimized the matrigel concentration for the 3D culture system and found the 3D culture system protected the SGNs against apoptosis, preserved the structure of spiral ganglion region, and promoted the sprouting and outgrowth of SGNs neurites. Next, we found the 3D culture system promoted growth cone growth as evidenced by a higher average number and a longer average length of filopodia and a larger growth cone area. 3D culture system also significantly elevated the synapse density of SGNs. Last, we found that the 3D culture system combined with neurotrophic factors had accumulated effects in promoting the neurites outgrowth compared with 3D culture or NFs treatment only groups. Together, we conclude that the 3D culture system preserves the structure and function of SGN in explant culture.

A molecular description of ligand binding to the two overlapping binding pockets of the nuclear vitamin D receptor (VDR): structure-function implications

PubMed Central

Mizwicki, Mathew T.; Menegaz, Danusa; Yaghmaei, Sepideh; Henry, Helen L.; Norman, Anthony W.

2010-01-01

Molecular modeling results indicate that the VDR contains two overlapping ligand binding pockets (LBP). Differential ligand stability and fractional occupancy of the two LBP has been physiochemically linked to the regulation of VDR-dependent genomic and non-genomic cellular responses. The purpose of this report is to develop an unbiased molecular modeling protocol that serves as a good starting point in simulating the dynamic interaction between 1α,25(OH)2-vitamin D3 (1,25D3) and the VDR LBP. To accomplish this goal, the flexible docking protocol developed allowed for flexibility in the VDR ligand and the VDR atoms that form the surfaces of the VDR LBP. This approach blindly replicated the 1,25D3 conformation and side-chain dynamics observed in the VDR x-ray structure. The results are also consistent with the previously published tenants of the vitamin D sterol (VDS)-VDR conformational ensemble model. Furthermore, we used flexible docking in combination with whole cell patch clamp electrophysiology and steroid competition assays to demonstrate that a) new non-vitamin D VDR ligands show a different pocket selectivity when compared to 1,25D3 that is qualitatively consistent with their ability to stimulate chloride channels and b) a new route of ligand binding provides a novel hypothesis describing the structural nuances that underlie hypercalceamia. PMID:20398762

New applications of a model of electromechanical impedance for SHM

NASA Astrophysics Data System (ADS)

Pavelko, Vitalijs

2014-03-01

The paper focuses on the further development of the model of the electromechanical impedance (EMI) of the piezoceramics transducer (PZT) and its application for aircraft structural health monitoring (SHM). There was obtained an expression of the electromechanical impedance common to any dimension of models (1D, 2D, 3D), and directly independent from imposed constraints. Determination of the dynamic response of the system "host structure - PZT", which is crucial for the practical application supposes the use of modal analysis. This allows to get a general tool to determine EMI regardless of the specific features of a particular application. Earlier there was considered the technology of separate determination of the dynamic response for the PZT and the structural element". Here another version that involves the joint modal analysis of the entire system "host structure - PZT" is presented. As a result, the dynamic response is obtained in the form of modal decomposition of transducer mechanical strains. The use of models for the free and constrained transducer, analysis of the impact of the adhesive layer to the EMI is demonstrated. In all cases there was analyzed the influence of the dimension of the model (2D and 3D). The validity of the model is confirmed by experimental studies. Correlation between the fatigue crack length in a thin-walled Al plate and EMI of embedded PZT was simulated and compared with test result.

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

NASA Astrophysics Data System (ADS)

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

1998-07-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gunár, Stanislav; Heinzel, Petr; Mackay, Duncan H.

2016-12-20

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

Cancer cells growing on perfused 3D collagen model produced higher reactive oxygen species level and were more resistant to cisplatin compared to the 2D model.

PubMed

Liu, Qingxi; Zhang, Zijiang; Liu, Yupeng; Cui, Zhanfeng; Zhang, Tongcun; Li, Zhaohui; Ma, Wenjian

2018-03-01

Three-dimensional (3D) collagen scaffold models, due to their ability to mimic the tissue and organ structure in vivo, have received increasing interest in drug discovery and toxicity evaluation. In this study, we developed a perfused 3D model and studied cellular response to cytotoxic drugs in comparison with traditional 2D cell cultures as evaluated by cancer drug cisplatin. Cancer cells grown in perfused 3D environments showed increased levels of reactive oxygen species (ROS) production compared to the 2D culture. As determined by growth analysis, cells in the 3D culture, after forming a spheroid, were more resistant to the cancer drug cisplatin compared to that of the 2D cell culture. In addition, 3D culturing cells showed elevated level of ROS, indicating a physiological change or the formation of a microenvironment that resembles tumor cells in vivo. These data revealed that cellular response to drugs for cells growing in 3D environments are dramatically different from that of 2D cultured cells. Thus, the perfused 3D collagen scaffold model we report here might be a potentially very useful tool for drug analysis.

Three-dimensional Cascaded Lattice Boltzmann Model for Thermal Convective Flows

NASA Astrophysics Data System (ADS)

Hajabdollahi, Farzaneh; Premnath, Kannan

2017-11-01

Fluid motion driven by thermal effects, such as due to buoyancy in differentially heated enclosures arise in several natural and industrial settings, whose understanding can be achieved via numerical simulations. Lattice Boltzmann (LB) methods are efficient kinetic computational approaches for coupled flow physics problems. In this study, we develop three-dimensional (3D) LB models based on central moments and multiple relaxation times for D3Q7 and D3Q15 lattices to solve the energy transport equations in a double distribution function approach. Their collision operators lead to a cascaded structure involving higher order terms resulting in improved stability. This is coupled to a central moment based LB flow solver with source terms. The new 3D cascaded LB models for the convective flows are first validated for natural convection of air driven thermally on two vertically opposite faces in a cubic cavity at different Rayleigh numbers against prior numerical and experimental data, which show good quantitative agreement. Then, the detailed structure of the 3D flow and thermal fields and the heat transfer rates at different Rayleigh numbers are analyzed and interpreted.

3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

ERIC Educational Resources Information Center

Meyer, Scott C.

2015-01-01

An upper-division undergraduate laboratory experiment is described that explores the structure/function relationship of protein domains, namely leucine zippers, through a molecular graphics computer program and physical models fabricated by 3D printing. By generating solvent accessible surfaces and color-coding hydrophobic, basic, and acidic amino…

Constructing Arguments with 3-D Printed Models

ERIC Educational Resources Information Center

McConnell, William; Dickerson, Daniel

2017-01-01

In this article, the authors describe a fourth-grade lesson where 3-D printing technologies were not only a stimulus for engagement but also served as a modeling tool providing meaningful learning opportunities. Specifically, fourth-grade students construct an argument that animals' external structures function to support survival in a particular…

2D and 3D separate and joint inversion of airborne ZTEM and ground AMT data: Synthetic model studies

NASA Astrophysics Data System (ADS)

Sasaki, Yutaka; Yi, Myeong-Jong; Choi, Jihyang

2014-05-01

The ZTEM (Z-axis Tipper Electromagnetic) method measures naturally occurring audio-frequency magnetic fields and obtains the tipper function that defines the relationship among the three components of the magnetic field. Since the anomalous tipper responses are caused by the presence of lateral resistivity variations, the ZTEM survey is most suited for detecting and delineating conductive bodies extending to considerable depths, such as graphitic dykes encountered in the exploration of unconformity type uranium deposit. Our simulations shows that inversion of ZTEM data can detect reasonably well multiple conductive dykes placed 1 km apart. One important issue regarding ZTEM inversion is the effect of the initial model, because homogeneous half-space and (1D) layered structures produce no responses. For the 2D model with multiple conductive dykes, the inversion results were useful for locating the dykes even when the initial model was not close to the true background resistivity. For general 3D structures, however, the resolution of the conductive bodies can be reduced considerably depending on the initial model. This is because the tipper magnitudes from 3D conductors are smaller due to boundary charges than the 2D responses. To alleviate this disadvantage of ZTEM surveys, we combined ZTEM and audio-frequency magnetotelluric (AMT) data. Inversion of sparse AMT data was shown to be effective in providing a good initial model for ZTEM inversion. Moreover, simultaneously inverting both data sets led to better results than the sequential approach by enabling to identify structural features that were difficult to resolve from the individual data sets.

Structural protein descriptors in 1-dimension and their sequence-based predictions.

PubMed

Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.

3D Realistic Radiative Hydrodynamic Modeling of a Moderate-Mass Star: Effects of Rotation

NASA Astrophysics Data System (ADS)

Kitiashvili, Irina; Kosovichev, Alexander G.; Mansour, Nagi N.; Wray, Alan A.

2018-01-01

Recent progress in stellar observations opens new perspectives in understanding stellar evolution and structure. However, complex interactions in the turbulent radiating plasma together with effects of magnetic fields and rotation make inferences of stellar properties uncertain. The standard 1D mixing-length-based evolutionary models are not able to capture many physical processes of stellar interior dynamics, but they provide an initial approximation of the stellar structure that can be used to initialize 3D time-dependent radiative hydrodynamics simulations, based on first physical principles, that take into account the effects of turbulence, radiation, and others. In this presentation we will show simulation results from a 3D realistic modeling of an F-type main-sequence star with mass 1.47 Msun, in which the computational domain includes the upper layers of the radiation zone, the entire convection zone, and the photosphere. The simulation results provide new insight into the formation and properties of the convective overshoot region, the dynamics of the near-surface, highly turbulent layer, the structure and dynamics of granulation, and the excitation of acoustic and gravity oscillations. We will discuss the thermodynamic structure, oscillations, and effects of rotation on the dynamics of the star across these layers.

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

PubMed

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

2017-09-01

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

Joint Inversion of 3d Mt/gravity/magnetic at Pisagua Fault.

NASA Astrophysics Data System (ADS)

Bascur, J.; Saez, P.; Tapia, R.; Humpire, M.

2017-12-01

This work shows the results of a joint inversion at Pisagua Fault using 3D Magnetotellurics (MT), gravity and regional magnetic data. The MT survey has a poor coverage of study area with only 21 stations; however, it allows to detect a low resistivity zone aligned with the Pisagua Fault trace that it is interpreted as a damage zone. The integration of gravity and magnetic data, which have more dense sampling and coverage, adds more detail and resolution to the detected low resistivity structure and helps to improve the structure interpretation using the resulted models (density, magnetic-susceptibility and electrical resistivity). The joint inversion process minimizes a multiple target function which includes the data misfit, model roughness and coupling norms (crossgradient and direct relations) for all geophysical methods considered (MT, gravity and magnetic). This process is solved iteratively using the Gauss-Newton method which updates the model of each geophysical method improving its individual data misfit, model roughness and the coupling with the other geophysical models. For solving the model updates of magnetic and gravity methods were developed dedicated 3D inversion software codes which include the coupling norms with additionals geophysical parameters. The model update of the 3D MT is calculated using an iterative method which sequentially filters the priority model and the output model of a single 3D MT inversion process for obtaining the resistivity model coupled solution with the gravity and magnetic methods.

A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

PubMed

Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Design and Validation of 3D Printed Complex Bone Models with Internal Anatomic Fidelity for Surgical Training and Rehearsal.

PubMed

Unger, Bertram J; Kraut, Jay; Rhodes, Charlotte; Hochman, Jordan

2014-01-01

Physical models of complex bony structures can be used for surgical skills training. Current models focus on surface rendering but suffer from a lack of internal accuracy due to limitations in the manufacturing process. We describe a technique for generating internally accurate rapid-prototyped anatomical models with solid and hollow structures from clinical and microCT data using a 3D printer. In a face validation experiment, otolaryngology residents drilled a cadaveric bone and its corresponding printed model. The printed bone models were deemed highly realistic representations across all measured parameters and the educational value of the models was strongly appreciated.

Augmented Reality in Scientific Publications-Taking the Visualization of 3D Structures to the Next Level.

PubMed

Wolle, Patrik; Müller, Matthias P; Rauh, Daniel

2018-03-16

The examination of three-dimensional structural models in scientific publications allows the reader to validate or invalidate conclusions drawn by the authors. However, either due to a (temporary) lack of access to proper visualization software or a lack of proficiency, this information is not necessarily available to every reader. As the digital revolution is quickly progressing, technologies have become widely available that overcome the limitations and offer to all the opportunity to appreciate models not only in 2D, but also in 3D. Additionally, mobile devices such as smartphones and tablets allow access to this information almost anywhere, at any time. Since access to such information has only recently become standard practice, we want to outline straightforward ways to incorporate 3D models in augmented reality into scientific publications, books, posters, and presentations and suggest that this should become general practice.

Protein structure database search and evolutionary classification.

PubMed

Yang, Jinn-Moon; Tung, Chi-Hua

2006-01-01

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture.

PubMed

Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez; Wolynes, Peter G; Onuchic, José N

2017-11-14

Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing (ChIP-Seq). We exploit the idea that chromosomes encode a 1D sequence of chromatin structural types. Interactions between these chromatin types determine the 3D structural ensemble of chromosomes through a process similar to phase separation. First, a neural network is used to infer the relation between the epigenetic marks present at a locus, as assayed by ChIP-Seq, and the genomic compartment in which those loci reside, as measured by DNA-DNA proximity ligation (Hi-C). Next, types inferred from this neural network are used as an input to an energy landscape model for chromatin organization [Minimal Chromatin Model (MiChroM)] to generate an ensemble of 3D chromosome conformations at a resolution of 50 kilobases (kb). After training the model, dubbed Maximum Entropy Genomic Annotation from Biomarkers Associated to Structural Ensembles (MEGABASE), on odd-numbered chromosomes, we predict the sequences of chromatin types and the subsequent 3D conformational ensembles for the even chromosomes. We validate these structural ensembles by using ChIP-Seq tracks alone to predict Hi-C maps, as well as distances measured using 3D fluorescence in situ hybridization (FISH) experiments. Both sets of experiments support the hypothesis of phase separation being the driving process behind compartmentalization. These findings strongly suggest that epigenetic marking patterns encode sufficient information to determine the global architecture of chromosomes and that de novo structure prediction for whole genomes may be increasingly possible. Copyright © 2017 the Author(s). Published by PNAS.

Towards a new technique to construct a 3D shear-wave velocity model based on converted waves

NASA Astrophysics Data System (ADS)

Hetényi, G.; Colavitti, L.

2017-12-01

A 3D model is essential in all branches of solid Earth sciences because geological structures can be heterogeneous and change significantly in their lateral dimension. The main target of this research is to build a crustal S-wave velocity structure in 3D. The currently popular methodologies to construct 3D shear-wave velocity models are Ambient Noise Tomography (ANT) and Local Earthquake Tomography (LET). Here we propose a new technique to map Earth discontinuities and velocities at depth based on the analysis of receiver functions. The 3D model is obtained by simultaneously inverting P-to-S converted waveforms recorded at a dense array. The individual velocity models corresponding to each trace are extracted from the 3D initial model along ray paths that are calculated using the shooting method, and the velocity model is updated during the inversion. We consider a spherical approximation of ray propagation using a global velocity model (iasp91, Kennett and Engdahl, 1991) for the teleseismic part, while we adopt Cartesian coordinates and a local velocity model for the crust. During the inversion process we work with a multi-layer crustal model for shear-wave velocity, with a flexible mesh for the depth of the interfaces. The RFs inversion represents a complex problem because the amplitude and the arrival time of different phases depend in a non-linear way on the depth of interfaces and the characteristics of the velocity structure. The solution we envisage to manage the inversion problem is the stochastic Neighbourhood Algorithm (NA, Sambridge, 1999), whose goal is to find an ensemble of models that sample the good data-fitting regions of a multidimensional parameter space. Depending on the studied area, this method can accommodate possible independent and complementary geophysical data (gravity, active seismics, LET, ANT, etc.), helping to reduce the non-linearity of the inversion. Our first focus of application is the Central Alps, where a 20-year long dataset of high-quality teleseismic events recorded at 81 stations is available, and we have high-resolution P-wave velocity model available (Diehl et al., 2009). We plan to extend the 3D shear-wave velocity inversion method to the entire Alpine domain in frame of the AlpArray project, and apply it to other areas with a dense network of broadband seismometers.

Fabrication and Deformation of 3D Multilayered Kirigami Microstructures.

PubMed

Humood, Mohammad; Shi, Yan; Han, Mengdi; Lefebvre, Joseph; Yan, Zheng; Pharr, Matt; Zhang, Yihui; Huang, Yonggang; Rogers, John A; Polycarpou, Andreas A

2018-03-01

Mechanically guided 3D microassembly with controlled compressive buckling represents a promising emerging route to 3D mesostructures in a broad range of advanced materials, including single-crystalline silicon (Si), of direct relevance to microelectronic devices. During practical applications, the assembled 3D mesostructures and microdevices usually undergo external mechanical loading such as out-of-plane compression, which can induce damage in or failure of the structures/devices. Here, the mechanical responses of a few mechanically assembled 3D kirigami mesostructures under flat-punch compression are studied through combined experiment and finite element analyses. These 3D kirigami mesostructures consisting of a bilayer of Si and SU-8 epoxy are formed through integration of patterned 2D precursors with a prestretched elastomeric substrate at predefined bonding sites to allow controlled buckling that transforms them into desired 3D configurations. In situ scanning electron microscopy measurement enables detailed studies of the mechanical behavior of these structures. Analysis of the load-displacement curves allows the measurement of the effective stiffness and elastic recovery of various 3D structures. The compression experiments indicate distinct regimes in the compressive force/displacement curves and reveals different geometry-dependent deformation for the structures. Complementary computational modeling supports the experimental findings and further explains the geometry-dependent deformation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

3D Structural Model of High-Performance Non-Fullerene Polymer Solar Cells as Revealed by High-Resolution AFM.

PubMed

Shi, Shaowei; Chen, Xiaofeng; Liu, Xubo; Wu, Xuefei; Liu, Feng; Zhang, Zhi-Guo; Li, Yongfang; Russell, Thomas P; Wang, Dong

2017-07-26

Rapid improvements in nonfullerene polymer solar cells (PSCs) have brought power conversion efficiencies to greater than 12%. To further improve device performance, a fundamental understanding of the correlations between structure and performance is essential. In this paper, based on a typical high-performance system consisting of J61(one donor-acceptor (D-A) copolymer of benzodithiophene and fluorine substituted benzotriazole) and ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone)-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), a 3D structural model is directly imaged by employing high-resolution atomic force microscopy (AFM). Hierarchical morphologies ranging from fiberlike crystallites, several nanometers in size, to a bicontinuous morphology, having domains tens of nanometers in size, are observed. A fibrillar interpenetrating networks of J61-rich domains embedded in a matrix comprised of a J61/ITIC is seen, reflecting the partial miscibility of J61 with ITIC. These hierarchical nanostructural characteristics are coupled to significantly enhanced exciton dissociation, and further contribute to photocurrent and final device performance.

Influence of georeference for saturated excess overland flow modelling using 3D volumetric soft geo-objects

NASA Astrophysics Data System (ADS)

Izham, Mohamad Yusoff; Muhamad Uznir, Ujang; Alias, Abdul Rahman; Ayob, Katimon; Wan Ruslan, Ismail

2011-04-01

Existing 2D data structures are often insufficient for analysing the dynamism of saturation excess overland flow (SEOF) within a basin. Moreover, all stream networks and soil surface structures in GIS must be preserved within appropriate projection plane fitting techniques known as georeferencing. Inclusion of 3D volumetric structure of the current soft geo-objects simulation model would offer a substantial effort towards representing 3D soft geo-objects of SEOF dynamically within a basin by visualising saturated flow and overland flow volume. This research attempts to visualise the influence of a georeference system towards the dynamism of overland flow coverage and total overland flow volume generated from the SEOF process using VSG data structure. The data structure is driven by Green-Ampt methods and the Topographic Wetness Index (TWI). VSGs are analysed by focusing on spatial object preservation techniques of the conformal-based Malaysian Rectified Skew Orthomorphic (MRSO) and the equidistant-based Cassini-Soldner projection plane under the existing geodetic Malaysian Revised Triangulation 1948 (MRT48) and the newly implemented Geocentric Datum for Malaysia (GDM2000) datum. The simulated result visualises deformation of SEOF coverage under different georeference systems via its projection planes, which delineate dissimilar computation of SEOF areas and overland flow volumes. The integration of Georeference, 3D GIS and the saturation excess mechanism provides unifying evidence towards successful landslide and flood disaster management through envisioning the streamflow generating process (mainly SEOF) in a 3D environment.

The development of a virtual 3D model of the renal corpuscle from serial histological sections for E-learning environments.

PubMed

Roth, Jeremy A; Wilson, Timothy D; Sandig, Martin

2015-01-01

Histology is a core subject in the anatomical sciences where learners are challenged to interpret two-dimensional (2D) information (gained from histological sections) to extrapolate and understand the three-dimensional (3D) morphology of cells, tissues, and organs. In gross anatomical education 3D models and learning tools have been associated with improved learning outcomes, but similar tools have not been created for histology education to visualize complex cellular structure-function relationships. This study outlines steps in creating a virtual 3D model of the renal corpuscle from serial, semi-thin, histological sections obtained from epoxy resin-embedded kidney tissue. The virtual renal corpuscle model was generated by digital segmentation to identify: Bowman's capsule, nuclei of epithelial cells in the parietal capsule, afferent arteriole, efferent arteriole, proximal convoluted tubule, distal convoluted tubule, glomerular capillaries, podocyte nuclei, nuclei of extraglomerular mesangial cells, nuclei of epithelial cells of the macula densa in the distal convoluted tubule. In addition to the imported images of the original sections the software generates, and allows for visualization of, images of virtual sections generated in any desired orientation, thus serving as a "virtual microtome". These sections can be viewed separately or with the 3D model in transparency. This approach allows for the development of interactive e-learning tools designed to enhance histology education of microscopic structures with complex cellular interrelationships. Future studies will focus on testing the efficacy of interactive virtual 3D models for histology education. © 2015 American Association of Anatomists.

Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods.

PubMed

Pilla, Kala Bharath; Gaalswyk, Kari; MacCallum, Justin L

2017-11-01

The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Imaging the Alpine Fault: preliminary results from a detailed 3D-VSP experiment at the DFDP-2 drill site in Whataroa, New Zealand

NASA Astrophysics Data System (ADS)

Lay, Vera; Bodenburg, Sascha; Buske, Stefan; Townend, John; Kellett, Richard; Savage, Martha; Schmitt, Douglas; Constantinou, Alexis; Eccles, Jennifer; Lawton, Donald; Hall, Kevin; Bertram, Malcolm; Gorman, Andrew

2017-04-01

The plate-bounding Alpine Fault in New Zealand is an 850 km long transpressive continental fault zone that is late in its earthquake cycle. The Deep Fault Drilling Project (DFDP) aims to deliver insight into the geological structure of this fault zone and its evolution by drilling and sampling the Alpine Fault at depth. Previously analysed 2D reflection seismic data image the main Alpine Fault reflector at a depth of 1.5-2.2 km with a dip of approximately 48° to the southeast below the DFDP-2 borehole. Additionally, there are indications of a more complex 3D fault structure with several fault branches which have not yet been clearly imaged in detail. For that reason we acquired a 3D-VSP seismic data set at the DFDP-2 drill site in January 2016. A zero-offset VSP and a walk-away VSP survey were conducted using a Vibroseis source. Within the borehole, a permanently installed "Distributed Acoustic Fibre Optic Cable" (down to 893 m) and a 3C Sercel slimwave tool (down to 400 m) were used to record the seismic wavefield. In addition, an array of 160 three-component receivers with a spacing of 10 m perpendicular and 20 m parallel to the main strike of the Alpine Fault was set up and moved successively along the valley to record reflections from the main Alpine Fault zone over a broad depth range and to derive a detailed 3D tomographic velocity model in the hanging wall. We will show a detailed 3D velocity model derived from first-arrival traveltime tomography. Subsets of the whole data set were analysed separately to estimate the corresponding ray coverage and the reliability of the observed features in the obtained velocity model. By testing various inversion parameters and starting models, we derived a detailed near-surface velocity model that reveals the significance of the old glacial valley structures. Hence, this new 3D model improves the velocity model derived previously from a 2D seismic profile line in that area. Furthermore, processing of the dense 3C data shows clear reflections on both inline and crossline profiles. Correlating single reflection events enables us to identify the origin of reflections recorded in the data and reveal their 3D character. This array data gives strong evidence for reflections coming from the side, possibly from the steeply dipping valley flanks. Finally, the data will be processed using advanced seismic imaging methods to derive a detailed structural image of the valley and the fault zone at depth. Thus, the results will provide a detailed basis for a seismic site characterization at the DFDP-2 drill site, that will be of crucial importance for further structural and geological investigations of the architecture of the Alpine Fault in this area.

Three-Dimensional Reconstruction of Coronary Arteries and Its Application in Localization of Coronary Artery Segments Corresponding to Myocardial Segments Identified by Transthoracic Echocardiography

PubMed Central

Zhong, Chunyan; Guo, Yanli; Huang, Haiyun; Tan, Liwen; Wu, Yi; Wang, Wenting

2013-01-01

Objectives. To establish 3D models of coronary arteries (CA) and study their application in localization of CA segments identified by Transthoracic Echocardiography (TTE). Methods. Sectional images of the heart collected from the first CVH dataset and contrast CT data were used to establish 3D models of the CA. Virtual dissection was performed on the 3D models to simulate the conventional sections of TTE. Then, we used 2D ultrasound, speckle tracking imaging (STI), and 2D ultrasound plus 3D CA models to diagnose 170 patients and compare the results to coronary angiography (CAG). Results. 3D models of CA distinctly displayed both 3D structure and 2D sections of CA. This simulated TTE imaging in any plane and showed the CA segments that corresponded to 17 myocardial segments identified by TTE. The localization accuracy showed a significant difference between 2D ultrasound and 2D ultrasound plus 3D CA model in the severe stenosis group (P < 0.05) and in the mild-to-moderate stenosis group (P < 0.05). Conclusions. These innovative modeling techniques help clinicians identify the CA segments that correspond to myocardial segments typically shown in TTE sectional images, thereby increasing the accuracy of the TTE-based diagnosis of CHD. PMID:24348745

Application of 3D-QSAR in the rational design of receptor ligands and enzyme inhibitors.

PubMed

Mor, Marco; Rivara, Silvia; Lodola, Alessio; Lorenzi, Simone; Bordi, Fabrizio; Plazzi, Pier Vincenzo; Spadoni, Gilberto; Bedini, Annalida; Duranti, Andrea; Tontini, Andrea; Tarzia, Giorgio

2005-11-01

Quantitative structure-activity relationships (QSARs) are frequently employed in medicinal chemistry projects, both to rationalize structure-activity relationships (SAR) for known series of compounds and to help in the design of innovative structures endowed with desired pharmacological actions. As a difference from the so-called structure-based drug design tools, they do not require the knowledge of the biological target structure, but are based on the comparison of drug structural features, thus being defined ligand-based drug design tools. In the 3D-QSAR approach, structural descriptors are calculated from molecular models of the ligands, as interaction fields within a three-dimensional (3D) lattice of points surrounding the ligand structure. These descriptors are collected in a large X matrix, which is submitted to multivariate analysis to look for correlations with biological activity. Like for other QSARs, the reliability and usefulness of the correlation models depends on the validity of the assumptions and on the quality of the data. A careful selection of compounds and pharmacological data can improve the application of 3D-QSAR analysis in drug design. Some examples of the application of CoMFA and CoMSIA approaches to the SAR study and design of receptor or enzyme ligands is described, pointing the attention to the fields of melatonin receptor ligands and FAAH inhibitors.

Fabrication and characterization of poly(propylene fumarate) scaffolds with controlled pore structures using 3-dimensional printing and injection molding.

PubMed

Lee, Kee-Won; Wang, Shanfeng; Lu, Lichun; Jabbari, Esmaiel; Currier, Bradford L; Yaszemski, Michael J

2006-10-01

Poly(propylene fumarate) (PPF) is an injectable, biodegradable polymer that has been used for fabricating preformed scaffolds in tissue engineering applications because of in situ crosslinking characteristics. Aiming for understanding the effects of pore structure parameters on bone tissue ingrowth, 3-dimensional (3D) PPF scaffolds with controlled pore architecture have been produced in this study from computer-aided design (CAD) models. We have created original scaffold models with 3 pore sizes (300, 600, and 900 microm) and randomly closed 0%, 10%, 20%, or 30% of total pores from the original models in 3 planes. PPF scaffolds were fabricated by a series steps involving 3D printing of support/build constructs, dissolving build materials, injecting PPF, and dissolving support materials. To investigate the effects of controlled pore size and interconnectivity on scaffolds, we compared the porosities between the models and PPF scaffolds fabricated thereby, examined pore morphologies in surface and cross-section using scanning electron microscopy, and measured permeability using the falling head conductivity test. The thermal properties of the resulting scaffolds as well as uncrosslinked PPF were determined by differential scanning calorimetry and thermogravimetric analysis. Average pore sizes and pore shapes of PPF scaffolds with 600- and 900-microm pores were similar to those of CAD models, but they depended on directions in those with 300-microm pores. Porosity and permeability of PPF scaffolds decreased as the number of closed pores in original models increased, particularly when the pore size was 300 microm as the result of low porosity and pore occlusion. These results show that 3D printing and injection molding technique can be applied to crosslinkable polymers to fabricate 3D porous scaffolds with controlled pore structures, porosity, and permeability using their CAD models.

Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model.

PubMed

Tedesco, Mariateresa; Frega, Monica; Martinoia, Sergio; Pesce, Mattia; Massobrio, Paolo

2015-10-18

Currently, large-scale networks derived from dissociated neurons growing and developing in vitro on extracellular micro-transducer devices are the gold-standard experimental model to study basic neurophysiological mechanisms involved in the formation and maintenance of neuronal cell assemblies. However, in vitro studies have been limited to the recording of the electrophysiological activity generated by bi-dimensional (2D) neural networks. Nonetheless, given the intricate relationship between structure and dynamics, a significant improvement is necessary to investigate the formation and the developing dynamics of three-dimensional (3D) networks. In this work, a novel experimental platform in which 3D hippocampal or cortical networks are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are realized by seeding neurons in a scaffold constituted of glass microbeads (30-40 µm in diameter) on which neurons are able to grow and form complex interconnected 3D assemblies. In this way, it is possible to design engineered 3D networks made up of 5-8 layers with an expected final cell density. The increasing complexity in the morphological organization of the 3D assembly induces an enhancement of the electrophysiological patterns displayed by this type of networks. Compared with the standard 2D networks, where highly stereotyped bursting activity emerges, the 3D structure alters the bursting activity in terms of duration and frequency, as well as it allows observation of more random spiking activity. In this sense, the developed 3D model more closely resembles in vivo neural networks.

Interfacing 3D Engineered Neuronal Cultures to Micro-Electrode Arrays: An Innovative In Vitro Experimental Model

PubMed Central

Tedesco, Mariateresa; Frega, Monica; Martinoia, Sergio; Pesce, Mattia; Massobrio, Paolo

2015-01-01

Currently, large-scale networks derived from dissociated neurons growing and developing in vitro on extracellular micro-transducer devices are the gold-standard experimental model to study basic neurophysiological mechanisms involved in the formation and maintenance of neuronal cell assemblies. However, in vitro studies have been limited to the recording of the electrophysiological activity generated by bi-dimensional (2D) neural networks. Nonetheless, given the intricate relationship between structure and dynamics, a significant improvement is necessary to investigate the formation and the developing dynamics of three-dimensional (3D) networks. In this work, a novel experimental platform in which 3D hippocampal or cortical networks are coupled to planar Micro-Electrode Arrays (MEAs) is presented. 3D networks are realized by seeding neurons in a scaffold constituted of glass microbeads (30-40 µm in diameter) on which neurons are able to grow and form complex interconnected 3D assemblies. In this way, it is possible to design engineered 3D networks made up of 5-8 layers with an expected final cell density. The increasing complexity in the morphological organization of the 3D assembly induces an enhancement of the electrophysiological patterns displayed by this type of networks. Compared with the standard 2D networks, where highly stereotyped bursting activity emerges, the 3D structure alters the bursting activity in terms of duration and frequency, as well as it allows observation of more random spiking activity. In this sense, the developed 3D model more closely resembles in vivo neural networks. PMID:26554533

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

PubMed

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

2018-04-16

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

Application of the Shell/3D Modeling Technique for the Analysis of Skin-Stiffener Debond Specimens

NASA Technical Reports Server (NTRS)

Krueger, Ronald; O'Brien, T. Kevin; Minguet, Pierre J.

2002-01-01

The application of a shell/3D modeling technique for the simulation of skin/stringer debond in a specimen subjected to three-point bending is demonstrated. The global structure was modeled with shell elements. A local three-dimensional model, extending to about three specimen thicknesses on either side of the delamination front was used to capture the details of the damaged section. Computed total strain energy release rates and mixed-mode ratios obtained from shell/13D simulations were in good agreement with results obtained from full solid models. The good correlations of the results demonstrated the effectiveness of the shell/3D modeling technique for the investigation of skin/stiffener separation due to delamination in the adherents.

A Quantitative Evaluation of SCEC Community Velocity Model Version 3.0

NASA Astrophysics Data System (ADS)

Chen, P.; Zhao, L.; Jordan, T. H.

2003-12-01

We present a systematic methodology for evaluating and improving 3D seismic velocity models using broadband waveform data from regional earthquakes. The operator that maps a synthetic waveform into an observed waveform is expressed in the Rytov form D(ω ) = {exp}[{i} ω δ τ {p}(ω ) - ω δ τ {q}(ω )]. We measure the phase delay time δ τ p(ω ) and the amplitude reduction time δ τ q(ω ) as a function of frequency ω using Gee & Jordan's [1992] isolation-filter technique, and we correct the data for frequency-dependent interference and frequency-independent source statics. We have applied this procedure to a set of small events in Southern California. Synthetic seismograms were computed using three types of velocity models: the 1D Standard Southern California Crustal Model (SoCaL) [Dreger & Helmberger, 1993], the 3D SCEC Community Velocity Model, Version 3.0 (CVM3.0) [Magistrale et al., 2000], and a set of path-averaged 1D models (A1D) extracted from CVM3.0 by horizontally averaging wave slownesses along source-receiver paths. The 3D synthetics were computed using K. Olsen's finite difference code. More than 1000 measurements were made on both P and S waveforms at frequencies ranging from 0.2 to 1 Hz. Overall, the 3D model provided a substantially better fit to the waveform data than either laterally homogeneous or path-dependent 1D models. Relative to SoCaL, CVM3.0 provided a variance reduction of about 64% in δ τ p, and 41% in δ τ q. Relative to A1D, the variance reduction is about 46% and 20%, respectively. The same set of measurements can be employed to invert for both seismic source properties and seismic velocity structures. Fully numerical methods are being developed to compute the Fréchet kernels for these measurements [L. Zhao et. al., this meeting]. This methodology thus provides a unified framework for regional studies of seismic sources and Earth structure in Southern California and elsewhere.

3D reconstruction of the structure of a residual limb for customising the design of a prosthetic socket.

PubMed

Shuxian, Zheng; Wanhua, Zhao; Bingheng, Lu

2005-01-01

Aiming at overcoming the limitations of the plaster-casting method in traditional prosthetic socket fabrication, the idea of reconstructing the 3D models for bones and skin of the residual limb is proposed. Given the two-dimensional obtained image through CT scanning, using image processing and reverse engineering techniques, the 3D solid model of the residual limb can be successfully reconstructed. The new approach can reproduce both the internal and the external structure of the residual limb. It can moreover avoid making a positive mould by the way of manual modifications. In addition to this, it can provide a scientific basis for the individualization of prosthetic socket design.

Influence of deflection on a fold-to-fault progression: field evidence from near Marietta, South Carolina

USGS Publications Warehouse

Clendenin, C.W.; Garihan, J.M.

2006-01-01

Four periods of deformation (D1-D4) are recognized in the Lion Park Road borrow pit near Marietta, South Carolina. Although each period is characterized by distinct structures, D3 produced two structural styles (D3a, D3b) resulting from layer-parallel shortening. D3a is characterized by detachment folding at the tip of an underlying thrust. D3b is a fold-to-fault progression that was localized by east-dipping, quartz-filled gash fractures. The fold-to-fault progression demonstrates the influence of a mechanical anisotropy on ramp development. The early stages of D3b were formed by deflection of northwest-directed, layer-parallel shortening and active, down-section propagation of folds and thrusts. Following connection with a splay of basal detachment, later D3b stages resulted from up-section movement that produced kink folding and a throughgoing thrust. This up-section movement deformed and modified the geometries of older, down-section structures. Detailed mesoscopic field observations, integrated with a combination of current thrust fault models, are used to interpret the D3b fold-to-fault progression. ?? 2006 Elsevier Ltd. All rights reserved.

Developing and Testing a 3d Cadastral Data Model a Case Study in Australia

NASA Astrophysics Data System (ADS)

Aien, A.; Kalantari, M.; Rajabifard, A.; Williamson, I. P.; Shojaei, D.

2012-07-01

Population growth, urbanization and industrialization place more pressure on land use with the need for increased space. To extend the use and functionality of the land, complex infrastructures are being built, both vertically and horizontally, layered and stacked. These three-dimensional (3D) developments affect the interests (Rights, Restrictions, and Responsibilities (RRRs)) attached to the underlying land. A 3D cadastre will assist in managing the effects of 3D development on a particular extent of land. There are many elements that contribute to developing a 3D cadastre, such as existing of 3D property legislations, 3D DBMS, 3D visualization. However, data modelling is one of the most important elements of a successful 3D cadastre. As architectural models of houses and high rise buildings help their users visualize the final product, 3D cadastre data model supports 3D cadastre users to understand the structure or behavior of the system and has a template that guides them to construct and implement the 3D cadastre. Many jurisdictions, organizations and software developers have built their own cadastral data model. Land Administration Domain Model (DIS-ISO 19152, The Netherlands) and ePlan (Intergovernmental Committee on Surveying and Mapping, Australia) are examples of existing data models. The variation between these data models is the result of different attitudes towards cadastres. However, there is a basic common thread among them all. Current cadastral data models use a 2D land-parcel concept and extend it to support 3D requirements. These data models cannot adequately manage and represent the spatial extent of 3D RRRs. Most of the current cadastral data models have been influenced by a very broad understanding of 3D cadastral concepts because better clarity in what needs to be represented and analysed in the cadastre needs to be established. This paper presents the first version of a 3D Cadastral Data Model (3DCDM_Version 1.0). 3DCDM models both the legal and physical extent of 3D properties and associated interests. The data model extends the traditional cadastral requirements to cover other applications such as urban planning and land valuation and taxation. A demonstration of a test system on the proposed data model is also presented. The test is based on a case study in Victoria, Australia to evaluate the effectiveness of the data model.

Application Perspective of 2D+SCALE Dimension

NASA Astrophysics Data System (ADS)

Karim, H.; Rahman, A. Abdul

2016-09-01

Different applications or users need different abstraction of spatial models, dimensionalities and specification of their datasets due to variations of required analysis and output. Various approaches, data models and data structures are now available to support most current application models in Geographic Information System (GIS). One of the focuses trend in GIS multi-dimensional research community is the implementation of scale dimension with spatial datasets to suit various scale application needs. In this paper, 2D spatial datasets that been scaled up as the third dimension are addressed as 2D+scale (or 3D-scale) dimension. Nowadays, various data structures, data models, approaches, schemas, and formats have been proposed as the best approaches to support variety of applications and dimensionality in 3D topology. However, only a few of them considers the element of scale as their targeted dimension. As the scale dimension is concerned, the implementation approach can be either multi-scale or vario-scale (with any available data structures and formats) depending on application requirements (topology, semantic and function). This paper attempts to discuss on the current and new potential applications which positively could be integrated upon 3D-scale dimension approach. The previous and current works on scale dimension as well as the requirements to be preserved for any given applications, implementation issues and future potential applications forms the major discussion of this paper.

Protein structure prediction with local adjust tabu search algorithm

PubMed Central

2014-01-01

Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

The role of three-dimensional printed models of skull in anatomy education: a randomized controlled trail.

PubMed

Chen, Shi; Pan, Zhouxian; Wu, Yanyan; Gu, Zhaoqi; Li, Man; Liang, Ze; Zhu, Huijuan; Yao, Yong; Shui, Wuyang; Shen, Zhen; Zhao, Jun; Pan, Hui

2017-04-03

Three-dimensional (3D) printed models represent educational tools of high quality compared with traditional teaching aids. Colored skull models were produced by 3D printing technology. A randomized controlled trial (RCT) was conducted to compare the learning efficiency of 3D printed skulls with that of cadaveric skulls and atlas. Seventy-nine medical students, who never studied anatomy, were randomized into three groups by drawing lots, using 3D printed skulls, cadaveric skulls, and atlas, respectively, to study the anatomical structures in skull through an introductory lecture and small group discussions. All students completed identical tests, which composed of a theory test and a lab test, before and after a lecture. Pre-test scores showed no differences between the three groups. In post-test, the 3D group was better than the other two groups in total score (cadaver: 29.5 [IQR: 25-33], 3D: 31.5 [IQR: 29-36], atlas: 27.75 [IQR: 24.125-32]; p = 0.044) and scores of lab test (cadaver: 14 [IQR: 10.5-18], 3D: 16.5 [IQR: 14.375-21.625], atlas: 14.5 [IQR: 10-18.125]; p = 0.049). Scores involving theory test, however, showed no difference between the three groups. In this RCT, an inexpensive, precise and rapidly-produced skull model had advantages in assisting anatomy study, especially in structure recognition, compared with traditional education materials.

The discovery of novel histone lysine methyltransferase G9a inhibitors (part 1): molecular design based on a series of substituted 2,4-diamino-7- aminoalkoxyquinazoline by molecular-docking-guided 3D quantitative structure-activity relationship studies.

PubMed

Feng, Taotao; Wang, Hai; Zhang, Xiaojin; Sun, Haopeng; You, Qidong

2014-06-01

Protein lysine methyltransferase G9a, which catalyzes methylation of lysine 9 of histone H3 (H3K9) and lysine 373 (K373) of p53, is overexpressed in human cancers. This suggests that small molecular inhibitors of G9a might be attractive antitumor agents. Herein we report our efforts on the design of novel G9a inhibitor based on the 3D quantitative structure-activity relationship (3D-QSAR) analysis of a series of 2,4-diamino-7-aminoalkoxyquinazolineas G9a inhibitors. The 3D-QSAR model was generated from 47 compounds using docking based molecular alignment. The best predictions were obtained with CoMFA standard model (q2 =0.700, r2 = 0.952) and CoMSIA model combined with steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor fields (q2 = 0.724, r2 =0.960). The structural requirements for substituted 2,4-diamino-7-aminoalkoxyquinazoline for G9a inhibitory activity can be obtained by analysing the COMSIA plots. Based on the information, six novel follow-up analogs were designed.

Investigations of the structure and electromagnetic interactions of few body systems

NASA Astrophysics Data System (ADS)

Harper, E. P.; Lehman, D. R.; Prats, F.

The structure and electromagnetic interactions of few-body systems were investigated. The structural properties of the very light nuclei are examined by developing theoretical models that begin from the basic interactions between the constituents and that are solved exactly (numerically), i.e., full three- or four-body dynamics. Such models are then used in an attempt to understand the details of the strong and electromagnetic interactions of the few-nucleon nuclei after the basic underlying reaction mechanisms are understood with simpler models. Topics included: (1) set up the equations for the low-energy photodisintegration of (3)He and (3)H including final-state interactions and the E1 plus E2 operators; (2) develop a unified picture of the p + d (YIELDS) (3)He + (GAMMA), p + d (YIELDS) (3)He + (PI) (0), p + d (YIELDS) (3)H + (PI) (+) reactions at intermediate energies; (3) calculate the elastic and inelastic (1(+) (YIELDS) 0 (+)) form factors for (6)Li with three-body ((ALPHA)NN) wave functions; (4) calculate static properties (RMS radius, magnetic moment, and quadrupole moment) of (6)Li with three-body wave functions; and (5) develop the theory for the coincidence reactions (6)Li(p,2p)n(ALPHA), (6)Li(e,e'p)n(ALPHA), and (6)Li(e,e'd)(ALPHA).

The application of artificial intelligence in the optimal design of mechanical systems

NASA Astrophysics Data System (ADS)

Poteralski, A.; Szczepanik, M.

2016-11-01

The paper is devoted to new computational techniques in mechanical optimization where one tries to study, model, analyze and optimize very complex phenomena, for which more precise scientific tools of the past were incapable of giving low cost and complete solution. Soft computing methods differ from conventional (hard) computing in that, unlike hard computing, they are tolerant of imprecision, uncertainty, partial truth and approximation. The paper deals with an application of the bio-inspired methods, like the evolutionary algorithms (EA), the artificial immune systems (AIS) and the particle swarm optimizers (PSO) to optimization problems. Structures considered in this work are analyzed by the finite element method (FEM), the boundary element method (BEM) and by the method of fundamental solutions (MFS). The bio-inspired methods are applied to optimize shape, topology and material properties of 2D, 3D and coupled 2D/3D structures, to optimize the termomechanical structures, to optimize parameters of composites structures modeled by the FEM, to optimize the elastic vibrating systems to identify the material constants for piezoelectric materials modeled by the BEM and to identify parameters in acoustics problem modeled by the MFS.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

D Reconstruction from Multi-View Medical X-Ray Images - Review and Evaluation of Existing Methods

NASA Astrophysics Data System (ADS)

Hosseinian, S.; Arefi, H.

2015-12-01

The 3D concept is extremely important in clinical studies of human body. Accurate 3D models of bony structures are currently required in clinical routine for diagnosis, patient follow-up, surgical planning, computer assisted surgery and biomechanical applications. However, 3D conventional medical imaging techniques such as computed tomography (CT) scan and magnetic resonance imaging (MRI) have serious limitations such as using in non-weight-bearing positions, costs and high radiation dose(for CT). Therefore, 3D reconstruction methods from biplanar X-ray images have been taken into consideration as reliable alternative methods in order to achieve accurate 3D models with low dose radiation in weight-bearing positions. Different methods have been offered for 3D reconstruction from X-ray images using photogrammetry which should be assessed. In this paper, after demonstrating the principles of 3D reconstruction from X-ray images, different existing methods of 3D reconstruction of bony structures from radiographs are classified and evaluated with various metrics and their advantages and disadvantages are mentioned. Finally, a comparison has been done on the presented methods with respect to several metrics such as accuracy, reconstruction time and their applications. With regards to the research, each method has several advantages and disadvantages which should be considered for a specific application.

Rigorous Approach in Investigation of Seismic Structure and Source Characteristicsin Northeast Asia: Hierarchical and Trans-dimensional Bayesian Inversion

NASA Astrophysics Data System (ADS)

Mustac, M.; Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.; Ford, S. R.; Sebastian, N.

2015-12-01

Conventional approaches to inverse problems suffer from non-linearity and non-uniqueness in estimations of seismic structures and source properties. Estimated results and associated uncertainties are often biased by applied regularizations and additional constraints, which are commonly introduced to solve such problems. Bayesian methods, however, provide statistically meaningful estimations of models and their uncertainties constrained by data information. In addition, hierarchical and trans-dimensional (trans-D) techniques are inherently implemented in the Bayesian framework to account for involved error statistics and model parameterizations, and, in turn, allow more rigorous estimations of the same. Here, we apply Bayesian methods throughout the entire inference process to estimate seismic structures and source properties in Northeast Asia including east China, the Korean peninsula, and the Japanese islands. Ambient noise analysis is first performed to obtain a base three-dimensional (3-D) heterogeneity model using continuous broadband waveforms from more than 300 stations. As for the tomography of surface wave group and phase velocities in the 5-70 s band, we adopt a hierarchical and trans-D Bayesian inversion method using Voronoi partition. The 3-D heterogeneity model is further improved by joint inversions of teleseismic receiver functions and dispersion data using a newly developed high-efficiency Bayesian technique. The obtained model is subsequently used to prepare 3-D structural Green's functions for the source characterization. A hierarchical Bayesian method for point source inversion using regional complete waveform data is applied to selected events from the region. The seismic structure and source characteristics with rigorously estimated uncertainties from the novel Bayesian methods provide enhanced monitoring and discrimination of seismic events in northeast Asia.

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua

2014-07-25

Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with themore » 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts are very similar, Flag-CSN pulldowns are a proper alternative to CSN preparation from erythrocytes.« less

Early experiences of planning stereotactic radiosurgery using 3D printed models of eyes with uveal melanomas

PubMed Central

Furdová, Alena; Sramka, Miron; Thurzo, Andrej; Furdová, Adriana

2017-01-01

Objective The objective of this study was to determine the use of 3D printed model of an eye with intraocular tumor for linear accelerator-based stereotactic radiosurgery. Methods The software for segmentation (3D Slicer) created virtual 3D model of eye globe with tumorous mass based on tissue density from computed tomography and magnetic resonance imaging data. A virtual model was then processed in the slicing software (Simplify3D®) and printed on 3D printer using fused deposition modeling technology. The material that was used for printing was polylactic acid. Results In 2015, stereotactic planning scheme was optimized with the help of 3D printed model of the patient’s eye with intraocular tumor. In the period 2001–2015, a group of 150 patients with uveal melanoma (139 choroidal melanoma and 11 ciliary body melanoma) were treated. The median tumor volume was 0.5 cm3 (0.2–1.6 cm3). The radiation dose was 35.0 Gy by 99% of dose volume histogram. Conclusion The 3D printed model of eye with tumor was helpful in planning the process to achieve the optimal scheme for irradiation which requires high accuracy of defining the targeted tumor mass and critical structures. PMID:28203052

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

NASA Astrophysics Data System (ADS)

Wang, Z.; Zipf, A.

2017-09-01

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

Upscaling of Solar Induced Chlorophyll Fluorescence from Leaf to Canopy Using the Dart Model and a Realistic 3d Forest Scene

NASA Astrophysics Data System (ADS)

Liu, W.; Atherton, J.; Mõttus, M.; MacArthur, A.; Teemu, H.; Maseyk, K.; Robinson, I.; Honkavaara, E.; Porcar-Castell, A.

2017-10-01

Solar induced chlorophyll a fluorescence (SIF) has been shown to be an excellent proxy of photosynthesis at multiple scales. However, the mechanical linkages between fluorescence and photosynthesis at the leaf level cannot be directly applied at canopy or field scales, as the larger scale SIF emission depends on canopy structure. This is especially true for the forest canopies characterized by high horizontal and vertical heterogeneity. While most of the current studies on SIF radiative transfer in plant canopies are based on the assumption of a homogeneous canopy, recently codes have been developed capable of simulation of fluorescence signal in explicit 3-D forest canopies. Here we present a canopy SIF upscaling method consisting of the integration of the 3-D radiative transfer model DART and a 3-D object model BLENDER. Our aim was to better understand the effect of boreal forest canopy structure on SIF for a spatially explicit forest canopy.

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2013-11-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform (DTP) with spatial data and query processing capabilities of Geographic Information Systems (GIS), multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized Directional Replacement Policy (DRP) based buffer management scheme. Polyhedron structures are used in Digital Surface Modeling (DSM) and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g. X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

Effective 3-D surface modeling for geographic information systems

NASA Astrophysics Data System (ADS)

Yüksek, K.; Alparslan, M.; Mendi, E.

2016-01-01

In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

Multi-Scale Analyses of Three Dimensional Woven Composite 3D Shell With a Cut Out Circle

NASA Astrophysics Data System (ADS)

Nguyen, Duc Hai; Wang, Hu

2018-06-01

A composite material are made by combining two or more constituent materials to obtain the desired material properties of each product type. The matrix material which can be polymer and fiber is used as reinforcing material. Currently, the polymer matrix is widely used in many different fields with differently designed structures such as automotive structures and aviation, aerospace, marine, etc. because of their excellent mechanical properties; in addition, they possess the high level of hardness and durability together with a significant reduction in weight compared to traditional materials. However, during design process of structure, there will be many interruptions created for the purpose of assembling the structures together or for many other design purposes. Therefore, when this structure is subject to load-bearing, its failure occurs at these interruptions due to stress concentration. This paper proposes multi-scale modeling and optimization strategies in evaluation of the effectiveness of fiber orientation in an E-glass/Epoxy woven composite 3D shell with circular holes at the center investigated by FEA results. A multi-scale model approach was developed to predict the mechanical behavior of woven composite 3D shell with circular holes at the center with different designs of material and structural parameters. Based on the analysis result of laminae, we have found that the 3D shell with fiber direction of 450 shows the best stress and strain bearing capacity. Thus combining several layers of 450 fiber direction in a multi-layer composite 3D shell reduces the stresses concentrated on the cuts of the structures.

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment

PubMed Central

2010-01-01

Background Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. Results We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. Conclusions In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets. PMID:21034488

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment.

PubMed

Capriles, Priscila V S Z; Guimarães, Ana C R; Otto, Thomas D; Miranda, Antonio B; Dardenne, Laurent E; Degrave, Wim M

2010-10-29

Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets.

Development and Assessment of a New 3D Neuroanatomy Teaching Tool for MRI Training

ERIC Educational Resources Information Center

Drapkin, Zachary A.; Lindgren, Kristen A.; Lopez, Michael J.; Stabio, Maureen E.

2015-01-01

A computerized three-dimensional (3D) neuroanatomy teaching tool was developed for training medical students to identify subcortical structures on a magnetic resonance imaging (MRI) series of the human brain. This program allows the user to transition rapidly between two-dimensional (2D) MRI slices, 3D object composites, and a combined model in…

[Non-biological 3D printed simulator for training in percutaneous nephro- lithotripsy].

PubMed

Alyaev, Yu G; Sirota, E S; Bezrukov, E A; Ali, S Kh; Bukatov, M D; Letunovskiy, A V; Byadretdinov, I Sh

2018-03-01

To develop a non-biological 3D printed simulator for training and preoperative planning in percutaneous nephrolithotripsy (PCNL), which allows doctors to master and perform all stages of the operation under ultrasound and fluoroscopy guidance. The 3D model was constructed using multislice spiral computed tomography (MSCT) images of a patient with staghorn urolithiasis. The MSCT data were processed and used to print the model. The simulator consisted of two parts: a non-biological 3D printed soft model of a kidney with reproduced intra-renal vascular and collecting systems and a printed 3D model of a human body. Using this 3D printed simulator, PCNL was performed in the interventional radiology operating room under ultrasound and fluoroscopy guidance. The designed 3D printed model of the kidney completely reproduces the individual features of the intra-renal structures of the particular patient. During the training, all the main stages of PCNL were performed successfully: the puncture, dilation of the nephrostomy tract, endoscopic examination, intra-renal lithotripsy. Our proprietary 3D-printed simulator is a promising development in the field of endourologic training and preoperative planning in the treatment of complicated forms of urolithiasis.

3D-QSAR studies on the inhibitory activity of trimethoprim analogues against Escherichia coli dihydrofolate reductase.

PubMed

Vijayaraj, Ramadoss; Devi, Mekapothula Lakshmi Vasavi; Subramanian, Venkatesan; Chattaraj, Pratim Kumar

2012-06-01

Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. To construct highly predictive 3D-QSAR models, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were used. The predicted models show statistically significant cross-validated and non-cross-validated correlation coefficient of r2 CV and r2 nCV, respectively. The final 3D-QSAR models were validated using structurally diverse test set compounds. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives. The results obtained from the CoMFA and CoMSIA study delineate the substituents on the trimethoprim analogues responsible for the enhanced potency and also provide valuable directions for the design of new trimethoprim analogues with improved affinity. © 2012 John Wiley & Sons A/S.

Simulation on the internal structure of three-dimensional proximal tibia under different mechanical environments.

PubMed

Fang, Juan; Gong, He; Kong, Lingyan; Zhu, Dong

2013-12-20

Bone can adjust its morphological structure to adapt to the changes of mechanical environment, i.e. the bone structure change is related to mechanical loading. This implies that osteoarthritis may be closely associated with knee joint deformity. The purposes of this paper were to simulate the internal bone mineral density (BMD) change in three-dimensional (3D) proximal tibia under different mechanical environments, as well as to explore the relationship between mechanical environment and bone morphological abnormity. The right proximal tibia was scanned with CT to reconstruct a 3D proximal tibia model in MIMICS, then it was imported to finite element software ANSYS to establish 3D finite element model. The internal structure of 3D proximal tibia of young normal people was simulated using quantitative bone remodeling theory in combination with finite element method, then based on the changing pattern of joint contact force on the tibial plateau in valgus knees, the mechanical loading was changed, and the simulated normal tibia structure was used as initial structure to simulate the internal structure of 3D proximal tibia for old people with 6° valgus deformity. Four regions of interest (ROIs) were selected in the proximal tibia to quantitatively analyze BMD and compare with the clinical measurements. The simulation results showed that the BMD distribution in 3D proximal tibia was consistent with clinical measurements in normal knees and that in valgus knees was consistent with the measurement of patients with osteoarthritis in clinics. It is shown that the change of mechanical environment is the main cause for the change of subchondral bone structure, and being under abnormal mechanical environment for a long time may lead to osteoarthritis. Besides, the simulation method adopted in this paper can more accurately simulate the internal structure of 3D proximal tibia under different mechanical environments. It helps to better understand the mechanism of osteoarthritis and provides theoretical basis and computational method for the prevention and treatment of osteoarthritis. It can also serve as basis for further study on periprosthetic BMD changes after total knee arthroplasty, and provide a theoretical basis for optimization design of prosthesis.

Simulation on the internal structure of three-dimensional proximal tibia under different mechanical environments

PubMed Central

2013-01-01

Background Bone can adjust its morphological structure to adapt to the changes of mechanical environment, i.e. the bone structure change is related to mechanical loading. This implies that osteoarthritis may be closely associated with knee joint deformity. The purposes of this paper were to simulate the internal bone mineral density (BMD) change in three-dimensional (3D) proximal tibia under different mechanical environments, as well as to explore the relationship between mechanical environment and bone morphological abnormity. Methods The right proximal tibia was scanned with CT to reconstruct a 3D proximal tibia model in MIMICS, then it was imported to finite element software ANSYS to establish 3D finite element model. The internal structure of 3D proximal tibia of young normal people was simulated using quantitative bone remodeling theory in combination with finite element method, then based on the changing pattern of joint contact force on the tibial plateau in valgus knees, the mechanical loading was changed, and the simulated normal tibia structure was used as initial structure to simulate the internal structure of 3D proximal tibia for old people with 6° valgus deformity. Four regions of interest (ROIs) were selected in the proximal tibia to quantitatively analyze BMD and compare with the clinical measurements. Results The simulation results showed that the BMD distribution in 3D proximal tibia was consistent with clinical measurements in normal knees and that in valgus knees was consistent with the measurement of patients with osteoarthritis in clinics. Conclusions It is shown that the change of mechanical environment is the main cause for the change of subchondral bone structure, and being under abnormal mechanical environment for a long time may lead to osteoarthritis. Besides, the simulation method adopted in this paper can more accurately simulate the internal structure of 3D proximal tibia under different mechanical environments. It helps to better understand the mechanism of osteoarthritis and provides theoretical basis and computational method for the prevention and treatment of osteoarthritis. It can also serve as basis for further study on periprosthetic BMD changes after total knee arthroplasty, and provide a theoretical basis for optimization design of prosthesis. PMID:24359345

Experimental Evidence for Improved Neuroimaging Interpretation Using Three-Dimensional Graphic Models

ERIC Educational Resources Information Center

Ruisoto, Pablo; Juanes, Juan Antonio; Contador, Israel; Mayoral, Paula; Prats-Galino, Alberto

2012-01-01

Three-dimensional (3D) or volumetric visualization is a useful resource for learning about the anatomy of the human brain. However, the effectiveness of 3D spatial visualization has not yet been assessed systematically. This report analyzes whether 3D volumetric visualization helps learners to identify and locate subcortical structures more…

Molecular cloning and 3D model of first cytochrome P450 from CYP3A subfamily in saltwater crocodile (Crocodylus porosus).

PubMed

Tabassum, Rabia

2017-10-18

Cytochrome P450s (CYPs) play critical role in oxidative metabolism of numerous xenobiotics and endogenous compounds. The first CYP3A subfamily member in saltwater crocodile has been cloned and modelled for three-dimensional (3D) structure. The full-length cDNA was obtained employing reverse transcription polymerase chain reaction (RT-PCR) strategy and rapid amplification of cDNA ends (RACE). The cDNA sequence of 1659 nucleotides includes 132 nucleotides from 5' untranslated region (UTR), an open reading frame of 1527 nucleotides encoding 509 amino acids designated as CYP3A163. The alignment of CYP3A163 sequence with CYP3A subfamily across the lineages exhibit the loss of 1 residue in birds and 7 residues in mammals in comparison to reptiles suggesting the adaptation processes during evolution. The amino acid identity of CYP3A163 with Alligator mississippiensis CYP3A77 and Homo sapiens CYP3A4 is 91% and 62% respectively. The 3D structure of CYP3A163 modelled using human CYP3A4 structure as a template with Phyre 2 software, represents high similarity with its functionally important motifs and catalytic domain. Both sequence and structure of CYP3A163 display the common and conserved features of CYP3A subfamily. Overall, this study provides primary molecular and structural data of CYP3A163 required to investigate the xenobiotic metabolism in saltwater crocodiles. Copyright © 2017 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Dolžan, Erazem; Vrabec, Marko

2015-04-01

From the earliest days of geological science, mountainous terrains with their extreme topographic relief and sparse to non-existent vegetation were utilized to a great advantage for gaining 3D insight into geological structure. But whereas Alpine vistas may offer perfect panoramic views of geology, the steep mountain slopes and vertical cliffs make it very time-consuming and difficult (if not impossible) to acquire quantitative mapping data such as precisely georeferenced traces of geological boundaries and attitudes of structural planes. We faced this problem in mapping the central Kamnik Alps of northern Slovenia, which are built up from Mid to Late Triassic succession of carbonate rocks. Polyphase brittle tectonic evolution, monotonous lithology and the presence of temporally and spatially irregular facies boundary between bedded platform carbonates and massive reef limestones considerably complicate the structural interpretation of otherwise perfectly exposed, but hardly accessible massif. We used Agisoft Photoscan Structure-from-Motion photogrammetric software to process a series of overlapping high-resolution (~0.25 m ground resolution) vertical aerial photographs originally acquired by the Geodetic Authority of the Republic of Slovenia for surveying purposes, to derive very detailed 3D triangular mesh models of terrain and associated photographic textures. Phototextures are crucial for geological interpretation of the models as they provide additional levels of detail and lithological information which is not resolvable from geometrical mesh models alone. We then exported the models to Paradigm Gocad software to refine and optimize the meshing. Structural interpretation of the models, including mapping of traces and surfaces of faults and stratigraphic boundaries and determining dips of structural planes, was performed in MVE Move suite which offers a range of useful tools for digital mapping and interpretation. Photogrammetric model was complemented by georeferenced geological field data acquired along mountain trail transects, mainly using the MVE Field Move software application. In our experience, vertical aerophotos were sufficient to generate precise surface models in all but the steepest mountain cliffs. Therefore, using existing vertical photoimagery (where available) is a very cost-effective alternative to organizing shooting campaigns with rented aircraft. For handling reasonably large models (cca 3 x 3 km, up to 10 million triangles), a low-end computer workstation with mid-range professional 3D graphic card is sufficient. The biggest bottleneck is the photogrammetric processing step which is time-consuming (10s of hrs) and has large RAM requirements, although those can be offset by dividing models into smaller parts. The major problem with geological modeling software like Gocad or Move is that it at present does not handle well projecting of phototextures. Whereas Photoscan-generated orthophotos can be vertically projected onto mesh models, this results in unacceptable distortions and gaps in subvertical or overhanging parts of the mountain cliff models. A real 3D UV texture mapping method, such as implemented in Photoscan, would be required to realistically model such areas. This limitations notwithstanding, digital geological mapping of photogrammetric models of mountains is a very promising, cost- and time-effective method for rapid structural interpretation and mapping of barren mountainous terrains, particularly when it is complemented by field measurements and observations.

Multi-Scale Modeling of an Integrated 3D Braided Composite with Applications to Helicopter Arm

NASA Astrophysics Data System (ADS)

Zhang, Diantang; Chen, Li; Sun, Ying; Zhang, Yifan; Qian, Kun

2017-10-01

A study is conducted with the aim of developing multi-scale analytical method for designing the composite helicopter arm with three-dimensional (3D) five-directional braided structure. Based on the analysis of 3D braided microstructure, the multi-scale finite element modeling is developed. Finite element analysis on the load capacity of 3D five-directional braided composites helicopter arm is carried out using the software ABAQUS/Standard. The influences of the braiding angle and loading condition on the stress and strain distribution of the helicopter arm are simulated. The results show that the proposed multi-scale method is capable of accurately predicting the mechanical properties of 3D braided composites, validated by the comparison the stress-strain curves of meso-scale RVCs. Furthermore, it is found that the braiding angle is an important factor affecting the mechanical properties of 3D five-directional braided composite helicopter arm. Based on the optimized structure parameters, the nearly net-shaped composite helicopter arm is fabricated using a novel resin transfer mould (RTM) process.

The impact of lateral variations in lithospheric thickness on glacial isostatic adjustment in West Antarctica

NASA Astrophysics Data System (ADS)

Nield, Grace A.; Whitehouse, Pippa L.; van der Wal, Wouter; Blank, Bas; O'Donnell, John Paul; Stuart, Graham W.

2018-04-01

Differences in predictions of Glacial Isostatic Adjustment (GIA) for Antarctica persist due to uncertainties in deglacial history and Earth rheology. The Earth models adopted in many GIA studies are defined by parameters that vary in the radial direction only and represent a global average Earth structure (referred to as 1D Earth models). Over-simplifying actual Earth structure leads to bias in model predictions in regions where Earth parameters differ significantly from the global average, such as West Antarctica. We investigate the impact of lateral variations in lithospheric thickness on GIA in Antarctica by carrying out two experiments that use different rheological approaches to define 3D Earth models that include spatial variations in lithospheric thickness. The first experiment defines an elastic lithosphere with spatial variations in thickness inferred from seismic studies. We compare the results from this 3D model with results derived from a 1D Earth model that has a uniform lithospheric thickness defined as the average of the 3D lithospheric thickness. Irrespective of deglacial history and sub-lithospheric mantle viscosity, we find higher gradients of present-day uplift rates (i.e. higher amplitude and shorter wavelength) in West Antarctica when using the 3D models, due to the thinner-than-1D-average lithosphere prevalent in this region. The second experiment uses seismically-inferred temperature as input to a power-law rheology thereby allowing the lithosphere to have a viscosity structure. Modelling the lithosphere with a power-law rheology results in behaviour that is equivalent to a thinner-lithosphere model, and it leads to higher amplitude and shorter wavelength deformation compared with the first experiment. We conclude that neglecting spatial variations in lithospheric thickness in GIA models will result in predictions of peak uplift and subsidence that are biased low in West Antarctica. This has important implications for ice-sheet modelling studies as the steeper gradients of uplift predicted from the more realistic 3D model may promote stability in marine-grounded regions of West Antarctica. Including lateral variations in lithospheric thickness, at least to the level of considering West and East Antarctica separately, is important for capturing short wavelength deformation and it has the potential to provide a better fit to GPS observations as well as an improved GIA correction for GRACE data.

Probing the structure of Leishmania donovani chagasi DHFR-TS: comparative protein modeling and protein-ligand interaction studies.

PubMed

Maganti, Lakshmi; Manoharan, Prabu; Ghoshal, Nanda

2010-09-01

Dihydrofolate reductase (DHFR) has been used successfully as a drug target in the area of anti-bacterial, anti-cancer and anti-malarial therapy. It also acts as a drug target for Leishmaniasis. Inhibition of DHFR leads to cell death through lack of thymine (nucleotide metabolism). Although the crystal structures of Leishmania major and Trypanosoma cruzi DHFR-thymidylate synthase (TS) have been resolved, to date there is no three-dimensional (3D)-structural information on DHFR-TS of Leishmania donovani chagasi, which causes visceral leishmaniasis. Our aim in this study was to model the 3D structure of L. donovani chagasi DHFR-TS, and to investigate the structural requirements for its inhibition. In this paper we describe a highly refined homology model of L. donovani chagasi DHFR-TS based on available crystallographic structures by using the Homology module of Insight II. Structural refinement and minimization of the generated L. donovani chagasi DHFR-TS model employed the Discover 3 module of Insight II and molecular dynamic simulations. The model was further validated through use of the PROCHECK, Verify_3D, PROSA, PSQS and ERRAT programs, which confirm that the model is reliable. Superimposition of the model structure with the templates L. major A chain, L. major B chain And T. cruzi A chain showed root mean square deviations of 0.69 A, 0.71 A and 1.11 A, respectively. Docking analysis of the L. donovani chagasi DHFR-TS model with methotrexate enabled us to identify specific residues, viz. Val156, Val30, Lys95, Lys75 and Arg97, within the L. donovani chagasi DHFR-TS binding pocket, that play an important role in ligand or substrate binding. Docking studies clearly indicated that these five residues are important determinants for binding as they have strong hydrogen bonding interactions with the ligand.

Hyperfine structure and isotope shift analysis of singly ionized titanium

NASA Astrophysics Data System (ADS)

Bouazza, Safa

2013-04-01

The even-parity low configuration system of Ti II has been considered on the basis of the experimental data found in the literature, and its fine structure has been reanalyzed by simultaneous parameterization of one- and two-body interactions for the model space (3d + 4s)3. Furthermore, the main one-electron hyperfine structure parameters for these configurations have been evaluated. For instance, for 3d24s1, a_{3{\\rm{d}}}^{01} = - {\\rm{63}}.{\\rm{2}}\\left( {{\\rm{3}}.{\\rm{1}}} \\right)\\,{\\rm{MHz}} and a_{4{\\rm{s}}}^{10} = - {\\rm{984}}.{\\rm{1}}\\left( {{\\rm{7}}.{\\rm{1}}} \\right)\\,{\\rm{MHz}} . Field shifts (FS) and specific mass shifts (SMS) of the main Ti II configurations are deduced by means of ab initio estimates combined with a small quantity of experimental isotope shift data available in the literature: FS(3d3) = -63.3 MHz, FS(3d24p1) = -49.7 MHz, FS(3d14s2) = 98.2 MHz, FS(4s24P1) = 163.4 MHz and SMS(3d3) = 1453.3 MHz, SMS(3d14s2) = -2179.7 MHz, …, referred to 3d24s1 for the pair Ti46-Ti48.

Synthesis, biological evaluation, and 3D QSAR study of 2-methyl-4-oxo-3-oxetanylcarbamic acid esters as N-acylethanolamine acid amidase (NAAA) inhibitors.

PubMed

Ponzano, Stefano; Berteotti, Anna; Petracca, Rita; Vitale, Romina; Mengatto, Luisa; Bandiera, Tiziano; Cavalli, Andrea; Piomelli, Daniele; Bertozzi, Fabio; Bottegoni, Giovanni

2014-12-11

N-(2-Oxo-3-oxetanyl)carbamic acid esters have recently been reported to be noncompetitive inhibitors of the N-acylethanolamine acid amidase (NAAA) potentially useful for the treatment of pain and inflammation. In the present study, we further explored the structure-activity relationships of the carbamic acid ester side chain of 2-methyl-4-oxo-3-oxetanylcarbamic acid ester derivatives. Additional favorable features in the design of potent NAAA inhibitors have been found together with the identification of a single digit nanomolar inhibitor. In addition, we devised a 3D QSAR using the atomic property field method. The model turned out to be able to account for the structural variability and was prospectively validated by designing, synthesizing, and testing novel inhibitors. The fairly good agreement between predictions and experimental potency values points to this 3D QSAR model as the first example of quantitative structure-activity relationships in the field of NAAA inhibitors.

Investigation of antigen-antibody interactions of sulfonamides with a monoclonal antibody in a fluorescence polarization immunoassay using 3D-QSAR models

USDA-ARS?s Scientific Manuscript database

A three-dimensional quantitative structure-activity relationship (3D-QSAR) model of sulfonamide analogs binding a monoclonal antibody (MAbSMR) produced against sulfamerazine was carried out by Distance Comparison (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular si...

3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

NASA Astrophysics Data System (ADS)

Doerschuk, Peter C.; Johnson, John E.

2000-11-01

A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

LCS-TA to identify similar fragments in RNA 3D structures.

PubMed

Wiedemann, Jakub; Zok, Tomasz; Milostan, Maciej; Szachniuk, Marta

2017-10-23

In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds' rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.

DREAM3D simulations of inner-belt dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cunningham, Gregory Scott

2015-05-26

A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of themore » problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.« less

Automated 3D structure composition for large RNAs

PubMed Central

Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

2012-01-01

Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

Quality assessment of protein model-structures based on structural and functional similarities

PubMed Central

2012-01-01

Background Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. Results GOBA - Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. Conclusions The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and one of CASP9, compared to the contest participants. Consequently, GOBA offers a novel single model quality assessment program that addresses the practical needs of biologists. In conjunction with other Model Quality Assessment Programs (MQAPs), it would prove useful for the evaluation of single protein models. PMID:22998498

Symbolic modeling of human anatomy for visualization and simulation

NASA Astrophysics Data System (ADS)

Pommert, Andreas; Schubert, Rainer; Riemer, Martin; Schiemann, Thomas; Tiede, Ulf; Hoehne, Karl H.

1994-09-01

Visualization of human anatomy in a 3D atlas requires both spatial and more abstract symbolic knowledge. Within our 'intelligent volume' model which integrates these two levels, we developed and implemented a semantic network model for describing human anatomy. Concepts for structuring (abstraction levels, domains, views, generic and case-specific modeling, inheritance) are introduced. Model, tools for generation and exploration and applications in our 3D anatomical atlas are presented and discussed.

Structured Light-Based 3D Reconstruction System for Plants.

PubMed

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

2015-07-29

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

Automated 3D architecture reconstruction from photogrammetric structure-and-motion: A case study of the One Pilla pagoda, Hanoi, Vienam

NASA Astrophysics Data System (ADS)

To, T.; Nguyen, D.; Tran, G.

2015-04-01

Heritage system of Vietnam has decline because of poor-conventional condition. For sustainable development, it is required a firmly control, space planning organization, and reasonable investment. Moreover, in the field of Cultural Heritage, the use of automated photogrammetric systems, based on Structure from Motion techniques (SfM), is widely used. With the potential of high-resolution, low-cost, large field of view, easiness, rapidity and completeness, the derivation of 3D metric information from Structure-and- Motion images is receiving great attention. In addition, heritage objects in form of 3D physical models are recorded not only for documentation issues, but also for historical interpretation, restoration, cultural and educational purposes. The study suggests the archaeological documentation of the "One Pilla" pagoda placed in Hanoi capital, Vietnam. The data acquired through digital camera Cannon EOS 550D, CMOS APS-C sensor 22.3 x 14.9 mm. Camera calibration and orientation were carried out by VisualSFM, CMPMVS (Multi-View Reconstruction) and SURE (Photogrammetric Surface Reconstruction from Imagery) software. The final result represents a scaled 3D model of the One Pilla Pagoda and displayed different views in MeshLab software.

Shape: A 3D Modeling Tool for Astrophysics.

PubMed

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

2011-04-01

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

3D Magnetic field modeling of a new superconducting synchronous machine using reluctance network method

NASA Astrophysics Data System (ADS)

Kelouaz, Moussa; Ouazir, Youcef; Hadjout, Larbi; Mezani, Smail; Lubin, Thiery; Berger, Kévin; Lévêque, Jean

2018-05-01

In this paper a new superconducting inductor topology intended for synchronous machine is presented. The studied machine has a standard 3-phase armature and a new kind of 2-poles inductor (claw-pole structure) excited by two coaxial superconducting coils. The air-gap spatial variation of the radial flux density is obtained by inserting a superconducting bulk, which deviates the magnetic field due to the coils. The complex geometry of this inductor usually needs 3D finite elements (FEM) for its analysis. However, to avoid a long computational time inherent to 3D FEM, we propose in this work an alternative modeling, which uses a 3D meshed reluctance network. The results obtained with the developed model are compared to 3D FEM computations as well as to measurements carried out on a laboratory prototype. Finally, a 3D FEM study of the shielding properties of the superconducting screen demonstrates the suitability of using a diamagnetic-like model of the superconducting screen.

Integrated VR platform for 3D and image-based models: a step toward interactive image-based virtual environments

NASA Astrophysics Data System (ADS)

Yoon, Jayoung; Kim, Gerard J.

2003-04-01

Traditionally, three dimension models have been used for building virtual worlds, and a data structure called the "scene graph" is often employed to organize these 3D objects in the virtual space. On the other hand, image-based rendering has recently been suggested as a probable alternative VR platform for its photo-realism, however, due to limited interactivity, it has only been used for simple navigation systems. To combine the merits of these two approaches to object/scene representations, this paper proposes for a scene graph structure in which both 3D models and various image-based scenes/objects can be defined, traversed, and rendered together. In fact, as suggested by Shade et al., these different representations can be used as different LOD's for a given object. For instance, an object might be rendered using a 3D model at close range, a billboard at an intermediate range, and as part of an environment map at far range. The ultimate objective of this mixed platform is to breath more interactivity into the image based rendered VE's by employing 3D models as well. There are several technical challenges in devising such a platform: designing scene graph nodes for various types of image based techniques, establishing criteria for LOD/representation selection, handling their transitions, implementing appropriate interaction schemes, and correctly rendering the overall scene. Currently, we have extended the scene graph structure of the Sense8's WorldToolKit, to accommodate new node types for environment maps billboards, moving textures and sprites, "Tour-into-the-Picture" structure, and view interpolated objects. As for choosing the right LOD level, the usual viewing distance and image space criteria are used, however, the switching between the image and 3D model occurs at a distance from the user where the user starts to perceive the object's internal depth. Also, during interaction, regardless of the viewing distance, a 3D representation would be used, it if exists. Before rendering, objects are conservatively culled from the view frustum using the representation with the largest volume. Finally, we carried out experiments to verify the theoretical derivation of the switching rule and obtained positive results.

Quantification of tumor morphology via 3D histology: application to oral cavity cancers

NASA Astrophysics Data System (ADS)

Doyle, Scott; Brandwein-Gensler, Margaret; Tomaszewski, John

2016-03-01

Traditional histopathology quantifies disease through the study of glass slides, i.e. two-dimensional samples that are representative of the overall process. We hypothesize that 3D reconstruction can enhance our understanding of histopathologic interpretations. To test this hypothesis, we perform a pilot study of the risk model for oral cavity cancer (OCC), which stratifies patients into low-, intermediate-, and high-risk for locoregional disease-free survival. Classification is based on study of hematoxylin and eosin (H and E) stained tissues sampled from the resection specimens. In this model, the Worst Pattern of Invasion (WPOI) is assessed, representing specific architectural features at the interface between cancer and non-cancer tissue. Currently, assessment of WPOI is based on 2D sections of tissue, representing complex 3D structures of tumor growth. We believe that by reconstructing a 3D model of tumor growth and quantifying the tumor-host interface, we can obtain important diagnostic information that is difficult to assess in 2D. Therefore, we introduce a pilot study framework for visualizing tissue architecture and morphology in 3D from serial sections of histopathology. This framework can be used to enhance predictive models for diseases where severity is determined by 3D biological structure. In this work we utilize serial H and E-stained OCC resections obtained from 7 patients exhibiting WPOI-3 (low risk of recurrence) through WPOI-5 (high risk of recurrence). A supervised classifier automatically generates a map of tumor regions on each slide, which are then co-registered using an elastic deformation algorithm. A smooth 3D model of the tumor region is generated from the registered maps, which is suitable for quantitative tumor interface morphology feature extraction. We report our preliminary models created with this system and suggest further enhancements to traditional histology scoring mechanisms that take spatial architecture into consideration.

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

The North Alpine Foreland Basin is situated in the northern front of the European Alps and extends over parts of France, Switzerland, Germany and Austria. It formed as a wedge shaped depression since the Tertiary in consequence of the Euro - Adriatic continental collision and the Alpine orogeny. The basin is filled with clastic sediments, the Molasse, originating from erosional processes of the Alps and underlain by Mesozoic sedimentary successions and a Paleozoic crystalline crust. For our study we have focused on the German part of the basin. To investigate the deep structure, the isostatic state and the load distribution of this region we have constructed a 3D structural model of the basin and the Alpine area using available depth and thickness maps, regional scale 3D structural models as well as seismic and well data for the sedimentary part. The crust (from the top Paleozoic down to the Moho (Grad et al. 2008)) has been considered as two-parted with a lighter upper crust and a denser lower crust; the partition has been calculated following the approach of isostatic equilibrium of Pratt (1855). By implementing a seismic Lithosphere-Asthenosphere-Boundary (LAB) (Tesauro 2009) the crustal scale model has been extended to the lithospheric-scale. The layer geometry and the assigned bulk densities of this starting model have been constrained by means of 3D gravity modelling (BGI, 2012). Afterwards the 3D load distribution has been calculated using a 3D finite element method. Our results show that the North Alpine Foreland Basin is not isostatically balanced and that the configuration of the crystalline crust strongly controls the gravity field in this area. Furthermore, our results show that the basin area is influenced by varying lateral load differences down to a depth of more than 150 km what allows a first order statement of the required compensating horizontal stress needed to prevent gravitational collapse of the system. BGI (2012). The International Gravimetric Bureau. IAG Geodesist's Handbook, 2012 - Journal of Geodesy, 86(10) Springer Grad, M., Tiira, T. and ESC Working Group (2009). The Moho depth map of 1 the European Plate. Geophysical Journal International 176(1): 279-292. Tesauro, M. (2009). An integrated study of the structure and thermomechanical properties of the European lithosphere. Department of Tectonics Faculty of Earth & Life Sciences. Amsterdam, Vrije Universiteit, Dissertation

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

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Ultrathin thermoresponsive self-folding 3D graphene

PubMed Central

Xu, Weinan; Qin, Zhao; Chen, Chun-Teh; Kwag, Hye Rin; Ma, Qinli; Sarkar, Anjishnu; Buehler, Markus J.; Gracias, David H.

2017-01-01

Graphene and other two-dimensional materials have unique physical and chemical properties of broad relevance. It has been suggested that the transformation of these atomically planar materials to three-dimensional (3D) geometries by bending, wrinkling, or folding could significantly alter their properties and lead to novel structures and devices with compact form factors, but strategies to enable this shape change remain limited. We report a benign thermally responsive method to fold and unfold monolayer graphene into predesigned, ordered 3D structures. The methodology involves the surface functionalization of monolayer graphene using ultrathin noncovalently bonded mussel-inspired polydopamine and thermoresponsive poly(N-isopropylacrylamide) brushes. The functionalized graphene is micropatterned and self-folds into ordered 3D structures with reversible deformation under a full control by temperature. The structures are characterized using spectroscopy and microscopy, and self-folding is rationalized using a multiscale molecular dynamics model. Our work demonstrates the potential to design and fabricate ordered 3D graphene structures with predictable shape and dynamics. We highlight applicability by encapsulating live cells and creating nonlinear resistor and creased transistor devices. PMID:28989963

Comparison of 3d Reconstruction Services and Terrestrial Laser Scanning for Cultural Heritage Documentation

NASA Astrophysics Data System (ADS)

Rasztovits, S.; Dorninger, P.

2013-07-01

Terrestrial Laser Scanning (TLS) is an established method to reconstruct the geometrical surface of given objects. Current systems allow for fast and efficient determination of 3D models with high accuracy and richness in detail. Alternatively, 3D reconstruction services are using images to reconstruct the surface of an object. While the instrumental expenses for laser scanning systems are high, upcoming free software services as well as open source software packages enable the generation of 3D models using digital consumer cameras. In addition, processing TLS data still requires an experienced user while recent web-services operate completely automatically. An indisputable advantage of image based 3D modeling is its implicit capability for model texturing. However, the achievable accuracy and resolution of the 3D models is lower than those of laser scanning data. Within this contribution, we investigate the results of automated web-services for image based 3D model generation with respect to a TLS reference model. For this, a copper sculpture was acquired using a laser scanner and using image series of different digital cameras. Two different webservices, namely Arc3D and AutoDesk 123D Catch were used to process the image data. The geometric accuracy was compared for the entire model and for some highly structured details. The results are presented and interpreted based on difference models. Finally, an economical comparison of the generation of the models is given considering the interactive and processing time costs.

New assessment of a structural alphabet

PubMed Central

de Brevern, Alexandre G.

2005-01-01

Summary A statistical analysis of the Protein Databank (PDB) structures had led us to define a set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one defined by the (Φ, Ψ) dihedral angles of 5 consecutive residues. Here, we analyze the effect of the enlargement of the PDB on the PBs’ definition. The results highlight the quality of the 3D approximation ensured by the PBs. These last could be of great interest in ab initio modeling. PMID:15996119

Using 3D printing techniques to create an anthropomorphic thorax phantom for medical imaging purposes.

PubMed

Hazelaar, Colien; van Eijnatten, Maureen; Dahele, Max; Wolff, Jan; Forouzanfar, Tymour; Slotman, Ben; Verbakel, Wilko F A R

2018-01-01

Imaging phantoms are widely used for testing and optimization of imaging devices without the need to expose humans to irradiation. However, commercially available phantoms are commonly manufactured in simple, generic forms and sizes and therefore do not resemble the clinical situation for many patients. Using 3D printing techniques, we created a life-size phantom based on a clinical CT scan of the thorax from a patient with lung cancer. It was assembled from bony structures printed in gypsum, lung structures consisting of airways, blood vessels >1 mm, and outer lung surface, three lung tumors printed in nylon, and soft tissues represented by silicone (poured into a 3D-printed mold). Kilovoltage x-ray and CT images of the phantom closely resemble those of the real patient in terms of size, shapes, and structures. Surface comparison using 3D models obtained from the phantom and the 3D models used for printing showed mean differences <1 mm for all structures. Tensile tests of the materials used for the phantom show that the phantom is able to endure radiation doses over 24,000 Gy. It is feasible to create an anthropomorphic thorax phantom using 3D printing and molding techniques. The phantom closely resembles a real patient in terms of spatial accuracy and is currently being used to evaluate x-ray-based imaging quality and positional verification techniques for radiotherapy. © 2017 American Association of Physicists in Medicine.

Model Package Report: Central Plateau Vadose Zone Geoframework Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Springer, Sarah D.

The purpose of the Central Plateau Vadose Zone (CPVZ) Geoframework model (GFM) is to provide a reasonable, consistent, and defensible three-dimensional (3D) representation of the vadose zone beneath the Central Plateau at the Hanford Site to support the Composite Analysis (CA) vadose zone contaminant fate and transport models. The GFM is a 3D representation of the subsurface geologic structure. From this 3D geologic model, exported results in the form of point, surface, and/or volumes are used as inputs to populate and assemble the various numerical model architectures, providing a 3D-layered grid that is consistent with the GFM. The objective ofmore » this report is to define the process used to produce a hydrostratigraphic model for the vadose zone beneath the Hanford Site Central Plateau and the corresponding CA domain.« less

3D bioprinting and its in vivo applications.

PubMed

Hong, Nhayoung; Yang, Gi-Hoon; Lee, JaeHwan; Kim, GeunHyung

2018-01-01

The purpose of 3D bioprinting technology is to design and create functional 3D tissues or organs in situ for in vivo applications. 3D cell-printing, or additive biomanufacturing, allows the selection of biomaterials and cells (bioink), and the fabrication of cell-laden structures in high resolution. 3D cell-printed structures have also been used for applications such as research models, drug delivery and discovery, and toxicology. Recently, numerous attempts have been made to fabricate tissues and organs by using various 3D printing techniques. However, challenges such as vascularization are yet to be solved. This article reviews the most commonly used 3D cell-printing techniques with their advantages and drawbacks. Furthermore, up-to-date achievements of 3D bioprinting in in vivo applications are introduced, and prospects for the future of 3D cell-printing technology are discussed. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 444-459, 2018. © 2017 Wiley Periodicals, Inc.

USM3D Predictions of Supersonic Nozzle Flow

NASA Technical Reports Server (NTRS)

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

2014-01-01

This study focused on the NASA Tetrahedral Unstructured Software System CFD code (USM3D) capability to predict supersonic plume flow. Previous studies, published in 2004 and 2009, investigated USM3D's results versus historical experimental data. This current study continued that comparison however focusing on the use of the volume souring to capture the shear layers and internal shock structure of the plume. This study was conducted using two benchmark axisymmetric supersonic jet experimental data sets. The study showed that with the use of volume sourcing, USM3D was able to capture and model a jet plume's shear layer and internal shock structure.

Improvements in mode-based waveform modeling and application to Eurasian velocity structure

NASA Astrophysics Data System (ADS)

Panning, M. P.; Marone, F.; Kim, A.; Capdeville, Y.; Cupillard, P.; Gung, Y.; Romanowicz, B.

2006-12-01

We introduce several recent improvements to mode-based 3D and asymptotic waveform modeling and examine how to integrate them with numerical approaches for an improved model of upper-mantle structure under eastern Eurasia. The first step in our approach is to create a large-scale starting model including shear anisotropy using Nonlinear Asymptotic Coupling Theory (NACT; Li and Romanowicz, 1995), which models the 2D sensitivity of the waveform to the great-circle path between source and receiver. We have recently improved this approach by implementing new crustal corrections which include a non-linear correction for the difference between the average structure of several large regions from the global model with further linear corrections to account for the local structure along the path between source and receiver (Marone and Romanowicz, 2006; Panning and Romanowicz, 2006). This model is further refined using a 3D implementation of Born scattering (Capdeville, 2005). We have made several recent improvements to this method, in particular introducing the ability to represent perturbations to discontinuities. While the approach treats all sensitivity as linear perturbations to the waveform, we have also experimented with a non-linear modification analogous to that used in the development of NACT. This allows us to treat large accumulated phase delays determined from a path-average approximation non-linearly, while still using the full 3D sensitivity of the Born approximation. Further refinement of shallow regions of the model is obtained using broadband forward finite-difference waveform modeling. We are also integrating a regional Spectral Element Method code into our tomographic modeling, allowing us to move beyond many assumptions inherent in the analytic mode-based approaches, while still taking advantage of their computational efficiency. Illustrations of the effects of these increasingly sophisticated steps will be presented.

Method for modeling post-mortem biometric 3D fingerprints

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

A 3D human tissue-engineered lung model to study influenza A infection.

PubMed

Bhowmick, Rudra; Derakhshan, Mina; Liang, Yurong; Ritchey, Jerry; Liu, Lin; Gappa-Fahlenkamp, Heather

2018-05-05

Influenza A virus (IAV) claims approximately 250,000-500,000 lives annually worldwide. Currently, there are a few in vitro models available to study IAV immunopathology. Monolayer cultures of cell lines and primary lung cells (2D cell culture) is the most commonly used tool, however, this system does not have the in vivo-like structure of the lung and immune responses to IAV as it lacks the three-dimensional (3D) tissue structure. To recapitulate the lung physiology in vitro, a system that contains multiple cell types within a 3D environment that allows cell movement and interaction, would provide a critical tool. In this study, as a first step in designing a 3D-Human Tissue-Engineering Lung Model (3D-HTLM), we described the 3D culture of primary human small airway epithelial cells (HSAEpCs), and determined the immunophenotype of this system in response to IAV infections. We constructed a 3D chitosan-collagen scaffold and cultured HSAEpCs on these scaffolds at air-liquid interface (ALI). These 3D cultures were compared with 2D-cultured HSAEpCs for viability, morphology, marker protein expression, and cell differentiation. Results showed that the 3D-cultured HSAEpCs at ALI yielded maximum viable cells and morphologically resembled the in vivo lower airway epithelium. There were also significant increases in aquaporin-5 and cytokeratin-14 expression for HSAEpCs cultured in 3D compared to 2D. The 3D culture system was used to study the infection of HSAEpCs with two major IAV strains, H1N1 and H3N2.The HSAEpCs showed distinct changes in marker protein expression, both at mRNA and protein levels, and the release of proinflammatory cytokines. This study is the first step in the development of the 3D-HTLM, which will have wide applicability in studying pulmonary pathophysiology and therapeutics development.

Leaving the structural ivory tower, assisted by interactive 3D PDF.

PubMed

Kumar, Pravin; Ziegler, Alexander; Grahn, Alexander; Hee, Chee Seng; Ziegler, Andreas

2010-08-01

The ability to embed interactive three-dimensional (3D) models into electronic publications in portable document format (PDF) greatly enhances the accessibility of molecular structures. Here, we report advances in this procedure and discuss what is needed to develop this format into a truly useful tool for the structural biology community as well as for readers who are less well trained in molecular visualization. Copyright 2010 Elsevier Ltd. All rights reserved.

Ultra small angle x-ray scattering in complex mixtures of triacylglycerols

NASA Astrophysics Data System (ADS)

Peyronel, Fernanda; Quinn, Bonnie; Marangoni, Alejandro G.; Pink, David A.

2014-11-01

Ultra-small angle x-ray scattering (USAXS) has been used to elucidate, in situ, the aggregation structure of unsheared model edible oils. Each system comprised one or two solid lipids and a combination of liquid lipids. The 3D nano- to micro-structures of each system were characterized. The length scale investigated, using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, ANL, ranged from 300 Å-10 µm. Using the Unified Fit model, level-1 analysis showed that the scatterers were 2D objects with either a smooth, a rough, or a diffuse surface. These 2D objects had an average radius of gyration Rg1 between 200-1500 Å. Level-2 analysis displayed a slope between -1 and -2. Use of the Guinier-Porod model gave s ≈ 1 thus showing that it was cylinders (TAGwoods) aggregating with fractal dimension 1 ≤ D2 ≤ 2. D2 = 1 is consistent with 1D structures formed from TAGwoods, while D2 = 2 implies that the TAGwoods had formed structures characteristic of diffusion or reaction limited cluster-cluster aggregation (DLCA/RLCA). These aggregates exhibited radii of gyration, Rg2, between 2500 and 6500 Å. Level-3 analyses showed diffuse surfaces, for most of the systems. These interpretations are in accord with theoretical models which studied crystalline nano-platelets (CNPs) coated with nano-scale layers arising from phase separation at the CNP surfaces. These layers could be due to either liquid-liquid phase separation with the CNPs coated, uniformly or non-uniformly, by a diffuse layer of TAGs, or solid-liquid phase separation with the CNPs coated by a rough layer of crystallites. A fundamental understanding of the self-organizing structures arising in these systems helps advance the characterization of fat crystal networks from nanometres to micrometres. This research can be used to design novel fat structures that use healthier fats via nano- and meso-scale structural engineering.

[Fitting of the reconstructed craniofacial hard and soft tissues based on 2-D digital radiographs].

PubMed

Feng, Yao-Pu; Qiao, Min; Zhou, Hong; Zhang, Yan-Ning; Si, Xin-Qin

2017-02-01

In this study, we reconstructed the craniofacial hard and soft tissues based on the data from digital cephalometric radiographs and laser scanning. The effective fitting of the craniofacial hard and soft tissues was performed in order to increase the level of orthognathic diagnosis and treatment, and promote the communication between doctors and patients. A small lead point was put on the face of a volunteer and frontal and lateral digital cephalometric radiographs were taken. 3-D reconstruction system of the craniofacial hard tissue based on 2-D digital radiograph was used to get the craniofacial hard tissue model by means of hard tissue deformation modeling. 3-D model of facial soft tissue was obtained by using laser scanning data. By matching the lead point coordinate, the hard tissue and soft tissue were fitted. The 3-D model of the craniofacial hard and soft tissues was rebuilt reflecting the real craniofacial tissue structure, and effective fitting of the craniofacial hard and soft tissues was realized. The effective reconstruction and fitting of the 3-D craniofacial structures have been realized, which lays a foundation for further orthognathic simulation and facial appearance prediction. The fitting result is reliable, and could be used in clinical practice.

ModeRNA server: an online tool for modeling RNA 3D structures.

PubMed

Rother, Magdalena; Milanowska, Kaja; Puton, Tomasz; Jeleniewicz, Jaroslaw; Rother, Kristian; Bujnicki, Janusz M

2011-09-01

The diverse functional roles of non-coding RNA molecules are determined by their underlying structure. ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program. ModeRNA server was implemented using the Python language and the Django web framework. It is freely available at http://iimcb.genesilico.pl/modernaserver. iamb@genesilico.pl.

Experimental evidence for improved neuroimaging interpretation using three-dimensional graphic models.

PubMed

Ruisoto, Pablo; Juanes, Juan Antonio; Contador, Israel; Mayoral, Paula; Prats-Galino, Alberto

2012-01-01

Three-dimensional (3D) or volumetric visualization is a useful resource for learning about the anatomy of the human brain. However, the effectiveness of 3D spatial visualization has not yet been assessed systematically. This report analyzes whether 3D volumetric visualization helps learners to identify and locate subcortical structures more precisely than classical cross-sectional images based on a two dimensional (2D) approach. Eighty participants were assigned to each experimental condition: 2D cross-sectional visualization vs. 3D volumetric visualization. Both groups were matched for age, gender, visual-spatial ability, and previous knowledge of neuroanatomy. Accuracy in identifying brain structures, execution time, and level of confidence in the response were taken as outcome measures. Moreover, interactive effects between the experimental conditions (2D vs. 3D) and factors such as level of competence (novice vs. expert), image modality (morphological and functional), and difficulty of the structures were analyzed. The percentage of correct answers (hit rate) and level of confidence in responses were significantly higher in the 3D visualization condition than in the 2D. In addition, the response time was significantly lower for the 3D visualization condition in comparison with the 2D. The interaction between the experimental condition (2D vs. 3D) and difficulty was significant, and the 3D condition facilitated the location of difficult images more than the 2D condition. 3D volumetric visualization helps to identify brain structures such as the hippocampus and amygdala, more accurately and rapidly than conventional 2D visualization. This paper discusses the implications of these results with regards to the learning process involved in neuroimaging interpretation. Copyright © 2012 American Association of Anatomists.

a Method of 3d Measurement and Reconstruction for Cultural Relics in Museums

NASA Astrophysics Data System (ADS)

Zheng, S.; Zhou, Y.; Huang, R.; Zhou, L.; Xu, X.; Wang, C.

2012-07-01

Three-dimensional measurement and reconstruction during conservation and restoration of cultural relics have become an essential part of a modem museum regular work. Although many kinds of methods including laser scanning, computer vision and close-range photogrammetry have been put forward, but problems still exist, such as contradiction between cost and good result, time and fine effect. Aimed at these problems, this paper proposed a structure-light based method for 3D measurement and reconstruction of cultural relics in museums. Firstly, based on structure-light principle, digitalization hardware has been built and with its help, dense point cloud of cultural relics' surface can be easily acquired. To produce accurate 3D geometry model from point cloud data, multi processing algorithms have been developed and corresponding software has been implemented whose functions include blunder detection and removal, point cloud alignment and merge, 3D mesh construction and simplification. Finally, high-resolution images are captured and the alignment of these images and 3D geometry model is conducted and realistic, accurate 3D model is constructed. Based on such method, a complete system including hardware and software are built. Multi-kinds of cultural relics have been used to test this method and results prove its own feature such as high efficiency, high accuracy, easy operation and so on.

Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

PubMed

Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

2010-01-01

A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Three-dimensional effects for radio frequency antenna modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, M.D.; Batchelor, D.B.; Stallings, D.C.

1994-10-15

Electromagnetic field calculations for radio frequency (rf) antennas in two dimensions (2-D) neglect finite antenna length effects as well as the feeders leading to the main current strap. The 2-D calculations predict that the return currents in the sidewalls of the antenna structure depend strongly on the plasma parameters, but this prediction is suspect because of experimental evidence. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform three-dimensional (3-D) modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused bymore » feeders to the main current strap and conducting sidewalls are considered. The modeling shows that the feeders affect the launched power spectrum in an indirect way by forcing the driven rf current to return in the antenna structure rather than the plasma, as in the 2-D model. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading predicted from that predicted in the 2-D model. For some plasma parameters, the combined 3-D effects can lead to a reduction in the predicted loading by as much as a factor of 2 from that given by the 2-D model, even with end-effect corrections for the 2-D model.« less

Three-dimensional effects for radio frequency antenna modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carter, M.D.; Batchelor, D.B.; Stallings, D.C.

1993-12-31

Electromagnetic field calculations for radio frequency (rf) antennas in two dimensions (2-D) neglect finite antenna length effects as well as the feeders leading to the main current strap. The 2-D calculations predict that the return currents in the sidewalls of the antenna structure depend strongly on the plasma parameters, but this prediction is suspect because of experimental evidence. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform three-dimensional (3-D) modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused bymore » feeders to the main current strap and conducting sidewalls are considered. The modeling shows that the feeders affect the launched power spectrum in an indirect way by forcing the driven rf current to return in the antenna structure rather than the plasma, as in the 2-D model. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading predicted from that predicted in the 2-D model. For some plasma parameters, the combined 3-D effects can lead to a reduction in the predicted loading by as much as a factor of 2 from that given by the 2-D model, even with end-effect corrections for the 2-D model.« less

Functional Equivalence Acceptance Testing of FUN3D for Entry Descent and Landing Applications

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; Wood, William A.; Kleb, William L.; Alter, Stephen J.; Glass, Christopher E.; Padilla, Jose F.; Hammond, Dana P.; White, Jeffery A.

2013-01-01

The functional equivalence of the unstructured grid code FUN3D to the the structured grid code LAURA (Langley Aerothermodynamic Upwind Relaxation Algorithm) is documented for applications of interest to the Entry, Descent, and Landing (EDL) community. Examples from an existing suite of regression tests are used to demonstrate the functional equivalence, encompassing various thermochemical models and vehicle configurations. Algorithm modifications required for the node-based unstructured grid code (FUN3D) to reproduce functionality of the cell-centered structured code (LAURA) are also documented. Challenges associated with computation on tetrahedral grids versus computation on structured-grid derived hexahedral systems are discussed.

Fractional modeling of viscoelasticity in 3D cerebral arteries and aneurysms

NASA Astrophysics Data System (ADS)

Yu, Yue; Perdikaris, Paris; Karniadakis, George Em

2016-10-01

We develop efficient numerical methods for fractional order PDEs, and employ them to investigate viscoelastic constitutive laws for arterial wall mechanics. Recent simulations using one-dimensional models [1] have indicated that fractional order models may offer a more powerful alternative for modeling the arterial wall response, exhibiting reduced sensitivity to parametric uncertainties compared with the integer-calculus-based models. Here, we study three-dimensional (3D) fractional PDEs that naturally model the continuous relaxation properties of soft tissue, and for the first time employ them to simulate flow structure interactions for patient-specific brain aneurysms. To deal with the high memory requirements and in order to accelerate the numerical evaluation of hereditary integrals, we employ a fast convolution method [2] that reduces the memory cost to O (log ⁡ (N)) and the computational complexity to O (Nlog ⁡ (N)). Furthermore, we combine the fast convolution with high-order backward differentiation to achieve third-order time integration accuracy. We confirm that in 3D viscoelastic simulations, the integer order models strongly depends on the relaxation parameters, while the fractional order models are less sensitive. As an application to long-time simulations in complex geometries, we also apply the method to modeling fluid-structure interaction of a 3D patient-specific compliant cerebral artery with an aneurysm. Taken together, our findings demonstrate that fractional calculus can be employed effectively in modeling complex behavior of materials in realistic 3D time-dependent problems if properly designed efficient algorithms are employed to overcome the extra memory requirements and computational complexity associated with the non-local character of fractional derivatives.

Fractional modeling of viscoelasticity in 3D cerebral arteries and aneurysms

PubMed Central

Perdikaris, Paris; Karniadakis, George Em

2017-01-01

We develop efficient numerical methods for fractional order PDEs, and employ them to investigate viscoelastic constitutive laws for arterial wall mechanics. Recent simulations using one-dimensional models [1] have indicated that fractional order models may offer a more powerful alternative for modeling the arterial wall response, exhibiting reduced sensitivity to parametric uncertainties compared with the integer-calculus-based models. Here, we study three-dimensional (3D) fractional PDEs that naturally model the continuous relaxation properties of soft tissue, and for the first time employ them to simulate flow structure interactions for patient-specific brain aneurysms. To deal with the high memory requirements and in order to accelerate the numerical evaluation of hereditary integrals, we employ a fast convolution method [2] that reduces the memory cost to O(log(N)) and the computational complexity to O(N log(N)). Furthermore, we combine the fast convolution with high-order backward differentiation to achieve third-order time integration accuracy. We confirm that in 3D viscoelastic simulations, the integer order models strongly depends on the relaxation parameters, while the fractional order models are less sensitive. As an application to long-time simulations in complex geometries, we also apply the method to modeling fluid–structure interaction of a 3D patient-specific compliant cerebral artery with an aneurysm. Taken together, our findings demonstrate that fractional calculus can be employed effectively in modeling complex behavior of materials in realistic 3D time-dependent problems if properly designed efficient algorithms are employed to overcome the extra memory requirements and computational complexity associated with the non-local character of fractional derivatives. PMID:29104310

Cochlear implant-related three-dimensional characteristics determined by micro-computed tomography reconstruction.

PubMed

Ni, Yusu; Dai, Peidong; Dai, Chunfu; Li, Huawei

2017-01-01

To explore the structural characteristics of the cochlea in three-dimensional (3D) detail using 3D micro-computed tomography (mCT) image reconstruction of the osseous labyrinth, with the aim of improving the structural design of electrodes, the selection of stimulation sites, and the effectiveness of cochlear implantation. Three temporal bones were selected from among adult donors' temporal bone specimens. A micro-CT apparatus (GE eXplore) was used to scan three specimens with a voxel resolution of 45 μm. We obtained about 460 slices/specimen, which produced abundant data. The osseous labyrinth images of three specimens were reconstructed from mCT. The cochlea and its spiral characteristics were measured precisely using Able Software 3D-DOCTOR. The 3D images of the osseous labyrinth, including the cochlea, vestibule, and semicircular canals, were reconstructed. The 3D models of the cochlea showed the spatial relationships and surface structural characteristics. Quantitative data concerning the cochlea and its spiral structural characteristics were analyzed with regard to cochlear implantation. The 3D reconstruction of mCT images clearly displayed the detailed spiral structural characteristics of the osseous labyrinth. Quantitative data regarding the cochlea and its spiral structural characteristics could help to improve electrode structural design, signal processing, and the effectiveness of cochlear implantation. Clin. Anat. 30:39-43, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Comparison of 3D point clouds produced by LIDAR and UAV photoscan in the Rochefort cave (Belgium)

NASA Astrophysics Data System (ADS)

Watlet, Arnaud; Triantafyllou, Antoine; Kaufmann, Olivier; Le Mouelic, Stéphane

2016-04-01

Amongst today's techniques that are able to produce 3D point clouds, LIDAR and UAV (Unmanned Aerial Vehicle) photogrammetry are probably the most commonly used. Both methods have their own advantages and limitations. LIDAR scans create high resolution and high precision 3D point clouds, but such methods are generally costly, especially for sporadic surveys. Compared to LIDAR, UAV (e.g. drones) are cheap and flexible to use in different kind of environments. Moreover, the photogrammetric processing workflow of digital images taken with UAV becomes easier with the rise of many affordable software packages (e.g. Agisoft, PhotoModeler3D, VisualSFM). We present here a challenging study made at the Rochefort Cave Laboratory (South Belgium) comprising surface and underground surveys. The site is located in the Belgian Variscan fold-and-thrust belt, a region that shows many karstic networks within Devonian limestone units. A LIDAR scan has been acquired in the main chamber of the cave (~ 15000 m³) to spatialize 3D point cloud of its inner walls and infer geological beds and structures. Even if the use of LIDAR instrument was not really comfortable in such caving environment, the collected data showed a remarkable precision according to few control points geometry. We also decided to perform another challenging survey of the same cave chamber by modelling a 3D point cloud using photogrammetry of a set of DSLR camera pictures taken from the ground and UAV pictures. The aim was to compare both techniques in terms of (i) implementation of data acquisition and processing, (ii) quality of resulting 3D points clouds (points density, field vs cloud recovery and points precision), (iii) their application for geological purposes. Through Rochefort case study, main conclusions are that LIDAR technique provides higher density point clouds with slightly higher precision than photogrammetry method. However, 3D data modeled by photogrammetry provide visible light spectral information for each modeled voxel and interpolated vertices that can be a useful attributes for clustering during data treatment. We thus illustrate such applications to the Rochefort cave by using both sources of 3D information to quantify the orientation of inaccessible geological structures (e.g. faults, tectonic and gravitational joints, and sediments bedding), cluster these structures using color information gathered from UAV's 3D point cloud and compare these data to structural data surveyed on the field. An additional drone photoscan was also conducted in the surface sinkhole giving access to the surveyed underground cavity to seek geological bodies' connections.

Identification of muscle necrosis in the mdx mouse model of Duchenne muscular dystrophy using three-dimensional optical coherence tomography

NASA Astrophysics Data System (ADS)

Klyen, Blake R.; Shavlakadze, Thea; Radley-Crabb, Hannah G.; Grounds, Miranda D.; Sampson, David D.

2011-07-01

Three-dimensional optical coherence tomography (3D-OCT) was used to image the structure and pathology of skeletal muscle tissue from the treadmill-exercised mdx mouse model of human Duchenne muscular dystrophy. Optical coherence tomography (OCT) images of excised muscle samples were compared with co-registered hematoxylin and eosin-stained and Evans blue dye fluorescence histology. We show, for the first time, structural 3D-OCT images of skeletal muscle dystropathology well correlated with co-located histology. OCT could identify morphological features of interest and necrotic lesions within the muscle tissue samples based on intrinsic optical contrast. These findings demonstrate the utility of 3D-OCT for the evaluation of small-animal skeletal muscle morphology and pathology, particularly for studies of mouse models of muscular dystrophy.

Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H

PubMed Central

Casillo, Angela; Ståhle, Jonas; Parrilli, Ermenegilda; Sannino, Filomena; Mitchell, Daniel E.; Pieretti, Giuseppina; Gibson, Matthew I.; Marino, Gennaro; Lanzetta, Rosa; Parrilli, Michelangelo; Widmalm, Göran; Tutino, Maria L.; Corsaro, Maria M.

2017-01-01

Colwellia psychrerythraea strain 34H, a Gram-negative bacterium isolated from Arctic marine sediments, is considered a model to study the adaptation to cold environments. Recently, we demonstrated that C. psychrerythraea 34H produces two different extracellular polysaccharides, a capsular polysaccharide and a medium released polysaccharide, which confer cryoprotection to the bacterium. In this study, we report the structure of an additional capsular polysaccharide produced by Colwellia grown at a different temperature. The structure was determined using chemical methods, and one- and two-dimensional NMR spectroscopy. The results showed a trisaccharide repeating unit made up of only amino-sugar residues: N-acetyl-galactosamine, 2,4-diacetamido-2,4,6-trideoxy-glucose (bacillosamine), and 2-acetamido-2-deoxyglucuronic acid with the following structure: →4)-β-d-GlcpNAcA-(1→3)-β-d-QuipNAc4NAc-(1→3)-β-d-GalpNAc-(1→. The 3D model, generated in accordance with 1H,1H-NOE NMR correlations and consisting of ten repeating units, shows a helical structure. In contrast with the other extracellular polysaccharides produced from Colwellia at 4 °C, this molecule displays only a low ice recrystallization inhibition activity. PMID:28161737

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

ERIC Educational Resources Information Center

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

2009-01-01

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

Trans-Dimensional Bayesian Imaging of 3-D Crustal and Upper Mantle Structure in Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.

2016-12-01

Imaging 3-D structures using stepwise inversions of ambient noise and receiver function data is now a routine work. Here, we carry out the inversion in the trans-dimensional and hierarchical extension of the Bayesian framework to obtain rigorous estimates of uncertainty and high-resolution images of crustal and upper mantle structures beneath Northeast (NE) Asia. The methods inherently account for data sensitivities by means of using adaptive parameterizations and treating data noise as free parameters. Therefore, parsimonious results from the methods are balanced out between model complexity and data fitting. This allows fully exploiting data information, preventing from over- or under-estimation of the data fit, and increases model resolution. In addition, the reliability of results is more rigorously checked through the use of Bayesian uncertainties. It is shown by various synthetic recovery tests that complex and spatially variable features are well resolved in our resulting images of NE Asia. Rayleigh wave phase and group velocity tomograms (8-70 s), a 3-D shear-wave velocity model from depth inversions of the estimated dispersion maps, and regional 3-D models (NE China, the Korean Peninsula, and the Japanese islands) from joint inversions with receiver function data of dense networks are presented. High-resolution models are characterized by a number of tectonically meaningful features. We focus our interpretation on complex patterns of sub-lithospheric low velocity structures that extend from back-arc regions to continental margins. We interpret the anomalies in conjunction with distal and distributed intraplate volcanoes in NE Asia. Further discussion on other imaged features will be presented.

3D braid scaffolds for regeneration of articular cartilage.

PubMed

Ahn, Hyunchul; Kim, Kyoung Ju; Park, Sook Young; Huh, Jeong Eun; Kim, Hyun Jeong; Yu, Woong-Ryeol

2014-06-01

Regenerating articular cartilage in vivo from cultured chondrocytes requires that the cells be cultured and implanted within a biocompatible, biodegradable scaffold. Such scaffolds must be mechanically stable; otherwise chondrocytes would not be supported and patients would experience severe pain. Here we report a new 3D braid scaffold that matches the anisotropic (gradient) mechanical properties of natural articular cartilage and is permissive to cell cultivation. To design an optimal structure, the scaffold unit cell was mathematically modeled and imported into finite element analysis. Based on this analysis, a 3D braid structure with gradient axial yarn distribution was designed and manufactured using a custom-built braiding machine. The mechanical properties of the 3D braid scaffold were evaluated and compared with simulated results, demonstrating that a multi-scale approach consisting of unit cell modeling and continuum analysis facilitates design of scaffolds that meet the requirements for mechanical compatibility with tissues. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reconstructing photorealistic 3D models from image sequence using domain decomposition method

NASA Astrophysics Data System (ADS)

Xiong, Hanwei; Pan, Ming; Zhang, Xiangwei

2009-11-01

In the fields of industrial design, artistic design and heritage conservation, physical objects are usually digitalized by reverse engineering through some 3D scanning methods. Structured light and photogrammetry are two main methods to acquire 3D information, and both are expensive. Even if these expensive instruments are used, photorealistic 3D models are seldom available. In this paper, a new method to reconstruction photorealistic 3D models using a single camera is proposed. A square plate glued with coded marks is used to place the objects, and a sequence of about 20 images is taken. From the coded marks, the images are calibrated, and a snake algorithm is used to segment object from the background. A rough 3d model is obtained using shape from silhouettes algorithm. The silhouettes are decomposed into a combination of convex curves, which are used to partition the rough 3d model into some convex mesh patches. For each patch, the multi-view photo consistency constraints and smooth regulations are expressed as a finite element formulation, which can be resolved locally, and the information can be exchanged along the patches boundaries. The rough model is deformed into a fine 3d model through such a domain decomposition finite element method. The textures are assigned to each element mesh, and a photorealistic 3D model is got finally. A toy pig is used to verify the algorithm, and the result is exciting.

Estimating 3D Leaf and Stem Shape of Nursery Paprika Plants by a Novel Multi-Camera Photography System

PubMed Central

Zhang, Yu; Teng, Poching; Shimizu, Yo; Hosoi, Fumiki; Omasa, Kenji

2016-01-01

For plant breeding and growth monitoring, accurate measurements of plant structure parameters are very crucial. We have, therefore, developed a high efficiency Multi-Camera Photography (MCP) system combining Multi-View Stereovision (MVS) with the Structure from Motion (SfM) algorithm. In this paper, we measured six variables of nursery paprika plants and investigated the accuracy of 3D models reconstructed from photos taken by four lens types at four different positions. The results demonstrated that error between the estimated and measured values was small, and the root-mean-square errors (RMSE) for leaf width/length and stem height/diameter were 1.65 mm (R2 = 0.98) and 0.57 mm (R2 = 0.99), respectively. The accuracies of the 3D model reconstruction of leaf and stem by a 28-mm lens at the first and third camera positions were the highest, and the number of reconstructed fine-scale 3D model shape surfaces of leaf and stem is the most. The results confirmed the practicability of our new method for the reconstruction of fine-scale plant model and accurate estimation of the plant parameters. They also displayed that our system is a good system for capturing high-resolution 3D images of nursery plants with high efficiency. PMID:27314348

Online 4d Reconstruction Using Multi-Images Available Under Open Access

NASA Astrophysics Data System (ADS)

Ioannides, M.; Hadjiprocopi, A.; Doulamis, N.; Doulamis, A.; Protopapadakis, E.; Makantasis, K.; Santos, P.; Fellner, D.; Stork, A.; Balet, O.; Julien, M.; Weinlinger, G.; Johnson, P. S.; Klein, M.; Fritsch, D.

2013-07-01

The advent of technology in digital cameras and their incorporation into virtually any smart mobile device has led to an explosion of the number of photographs taken every day. Today, the number of images stored online and available freely has reached unprecedented levels. It is estimated that in 2011, there were over 100 billion photographs stored in just one of the major social media sites. This number is growing exponentially. Moreover, advances in the fields of Photogrammetry and Computer Vision have led to significant breakthroughs such as the Structure from Motion algorithm which creates 3D models of objects using their twodimensional photographs. The existence of powerful and affordable computational machinery not only the reconstruction of complex structures but also entire cities. This paper illustrates an overview of our methodology for producing 3D models of Cultural Heritage structures such as monuments and artefacts from 2D data (pictures, video), available on Internet repositories, social media, Google Maps, Bing, etc. We also present new approaches to semantic enrichment of the end results and their subsequent export to Europeana, the European digital library, for integrated, interactive 3D visualisation within regular web browsers using WebGl and X3D. Our main goal is to enable historians, architects, archaeologists, urban planners and affiliated professionals to reconstruct views of historical structures from millions of images floating around the web and interact with them.

2D- and 3D-quantitative structure-activity relationship studies for a series of phenazine N,N'-dioxide as antitumour agents.

PubMed

Cunha, Jonathan Da; Lavaggi, María Laura; Abasolo, María Inés; Cerecetto, Hugo; González, Mercedes

2011-12-01

Hypoxic regions of tumours are associated with increased resistance to radiation and chemotherapy. Nevertheless, hypoxia has been used as a tool for specific activation of some antitumour prodrugs, named bioreductive agents. Phenazine dioxides are an example of such bioreductive prodrugs. Our 2D-quantitative structure activity relationship studies established that phenazine dioxides electronic and lipophilic descriptors are related to survival fraction in oxia or in hypoxia. Additionally, statistically significant models, derived by partial least squares, were obtained between survival fraction in oxia and comparative molecular field analysis standard model (r² = 0.755, q² = 0.505 and F = 26.70) or comparative molecular similarity indices analysis-combined steric and electrostatic fields (r² = 0.757, q² = 0.527 and F = 14.93), and survival fraction in hypoxia and comparative molecular field analysis standard model (r² = 0.736, q² = 0.521 and F = 18.63) or comparative molecular similarity indices analysis-hydrogen bond acceptor field (r² = 0.858, q² = 0.737 and F = 27.19). Categorical classification was used for the biological parameter selective cytotoxicity emerging also good models, derived by soft independent modelling of class analogy, with both comparative molecular field analysis standard model (96% of overall classification accuracy) and comparative molecular similarity indices analysis-steric field (92% of overall classification accuracy). 2D- and 3D-quantitative structure-activity relationships models provided important insights into the chemical and structural basis involved in the molecular recognition process of these phenazines as bioreductive agents and should be useful for the design of new structurally related analogues with improved potency. © 2011 John Wiley & Sons A/S.

Directing three-dimensional multicellular morphogenesis by self-organization of vascular mesenchymal cells in hyaluronic acid hydrogels.

PubMed

Zhu, Xiaolu; Gojgini, Shiva; Chen, Ting-Hsuan; Fei, Peng; Dong, Siyan; Ho, Chih-Ming; Segura, Tatiana

2017-01-01

Physical scaffolds are useful for supporting cells to form three-dimensional (3D) tissue. However, it is non-trivial to develop a scheme that can robustly guide cells to self-organize into a tissue with the desired 3D spatial structures. To achieve this goal, the rational regulation of cellular self-organization in 3D extracellular matrix (ECM) such as hydrogel is needed. In this study, we integrated the Turing reaction-diffusion mechanism with the self-organization process of cells and produced multicellular 3D structures with the desired configurations in a rational manner. By optimizing the components of the hydrogel and applying exogenous morphogens, a variety of multicellular 3D architectures composed of multipotent vascular mesenchymal cells (VMCs) were formed inside hyaluronic acid (HA) hydrogels. These 3D architectures could mimic the features of trabecular bones and multicellular nodules. Based on the Turing reaction-diffusion instability of morphogens and cells, a theoretical model was proposed to predict the variations observed in 3D multicellular structures in response to exogenous factors. It enabled the feasibility to obtain diverse types of 3D multicellular structures by addition of Noggin and/or BMP2. The morphological consistency between the simulation prediction and experimental results probably revealed a Turing-type mechanism underlying the 3D self-organization of VMCs in HA hydrogels. Our study has provided new ways to create a variety of self-organized 3D multicellular architectures for regenerating biomaterial and tissues in a Turing mechanism-based approach.

Two-dimensional confinement of 3d{1} electrons in LaTiO_{3}/LaAlO{3} multilayers.

PubMed

Seo, S S A; Han, M J; Hassink, G W J; Choi, W S; Moon, S J; Kim, J S; Susaki, T; Lee, Y S; Yu, J; Bernhard, C; Hwang, H Y; Rijnders, G; Blank, D H A; Keimer, B; Noh, T W

2010-01-22

We report spectroscopic ellipsometry measurements of the anisotropy of the interband transitions parallel and perpendicular to the planes of (LaTiO3)n(LaAlO3)5 multilayers with n=1-3. These provide direct information about the electronic structure of the two-dimensional (2D) 3d{1} state of the Ti ions. In combination with local density approximation, including a Hubbard U calculation, we suggest that 2D confinement in the TiO2 slabs lifts the degeneracy of the t{2g} states leaving only the planar d{xy} orbitals occupied. We outline that these multilayers can serve as a model system for the study of the t{2g} 2D Hubbard model.

Web3DMol: interactive protein structure visualization based on WebGL.

PubMed

Shi, Maoxiang; Gao, Juntao; Zhang, Michael Q

2017-07-03

A growing number of web-based databases and tools for protein research are being developed. There is now a widespread need for visualization tools to present the three-dimensional (3D) structure of proteins in web browsers. Here, we introduce our 3D modeling program-Web3DMol-a web application focusing on protein structure visualization in modern web browsers. Users submit a PDB identification code or select a PDB archive from their local disk, and Web3DMol will display and allow interactive manipulation of the 3D structure. Featured functions, such as sequence plot, fragment segmentation, measure tool and meta-information display, are offered for users to gain a better understanding of protein structure. Easy-to-use APIs are available for developers to reuse and extend Web3DMol. Web3DMol can be freely accessed at http://web3dmol.duapp.com/, and the source code is distributed under the MIT license. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mapping and modeling the urban landscape in Bangkok, Thailand: Physical-spectral-spatial relations of population-environmental interactions

NASA Astrophysics Data System (ADS)

Shao, Yang

This research focuses on the application of remote sensing, geographic information systems, statistical modeling, and spatial analysis to examine the dynamics of urban land cover, urban structure, and population-environment interactions in Bangkok, Thailand, with an emphasis on rural-to-urban migration from rural Nang Rong District, Northeast Thailand to the primate city of Bangkok. The dissertation consists of four main sections: (1) development of remote sensing image classification and change-detection methods for characterizing imperviousness for Bangkok, Thailand from 1993-2002; (2) development of 3-D urban mapping methods, using high spatial resolution IKONOS satellite images, to assess high-rises and other urban structures; (3) assessment of urban spatial structure from 2-D and 3-D perspectives; and (4) an analysis of the spatial clustering of migrants from Nang Rong District in Bangkok and the neighborhood environments of migrants' locations. Techniques are developed to improve the accuracy of the neural network classification approach for the analysis of remote sensing data, with an emphasis on the spectral unmixing problem. The 3-D building heights are derived using the shadow information on the high-resolution IKONOS image. The results from the 2-D and 3-D mapping are further examined to assess urban structure and urban feature identification. This research contributes to image processing of remotely-sensed images and urban studies. The rural-urban migration process and migrants' settlement patterns are examined using spatial statistics, GIS, and remote sensing perspectives. The results show that migrants' spatial clustering in urban space is associated with the source village and a number of socio-demographic variables. In addition, the migrants' neighborhood environments in urban setting are modeled using a set of geographic and socio-demographic variables, and the results are scale-dependent.

3D Reconstruction of Space Objects from Multi-Views by a Visible Sensor

PubMed Central

Zhang, Haopeng; Wei, Quanmao; Jiang, Zhiguo

2017-01-01

In this paper, a novel 3D reconstruction framework is proposed to recover the 3D structural model of a space object from its multi-view images captured by a visible sensor. Given an image sequence, this framework first estimates the relative camera poses and recovers the depths of the surface points by the structure from motion (SFM) method, then the patch-based multi-view stereo (PMVS) algorithm is utilized to generate a dense 3D point cloud. To resolve the wrong matches arising from the symmetric structure and repeated textures of space objects, a new strategy is introduced, in which images are added to SFM in imaging order. Meanwhile, a refining process exploiting the structural prior knowledge that most sub-components of artificial space objects are composed of basic geometric shapes is proposed and applied to the recovered point cloud. The proposed reconstruction framework is tested on both simulated image datasets and real image datasets. Experimental results illustrate that the recovered point cloud models of space objects are accurate and have a complete coverage of the surface. Moreover, outliers and points with severe noise are effectively filtered out by the refinement, resulting in an distinct improvement of the structure and visualization of the recovered points. PMID:28737675

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Recognizing 3 D Objects from 2D Images Using Structural Knowledge Base of Genetic Views

DTIC Science & Technology

1988-08-31

technical report. [BIE85] I. Biederman , "Human image understanding: Recent research and a theory", Computer Vision, Graphics, and Image Processing, vol...model bases", Technical Report 87-85, COINS Dept, University of Massachusetts, Amherst, MA 01003, August 1987 . [BUR87b) Burns, J. B. and L. J. Kitchen...34Recognition in 2D images of 3D objects from large model bases using prediction hierarchies", Proc. IJCAI-10, 1987 . [BUR891 J. B. Burns, forthcoming

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

PubMed Central

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-01-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search. PMID:15215446

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

PubMed

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-07-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

A 3D TCAD simulation of a thermoelectric module configured for thermoelectric power generation, cooling and heating

NASA Astrophysics Data System (ADS)

Gould, C. A.; Shammas, N. Y. A.; Grainger, S.; Taylor, I.; Simpson, K.

2012-06-01

This paper documents the 3D modeling and simulation of a three couple thermoelectric module using the Synopsys Technology Computer Aided Design (TCAD) semiconductor simulation software. Simulation results are presented for thermoelectric power generation, cooling and heating, and successfully demonstrate the basic thermoelectric principles. The 3D TCAD simulation model of a three couple thermoelectric module can be used in the future to evaluate different thermoelectric materials, device structures, and improve the efficiency and performance of thermoelectric modules.

Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series.

PubMed

Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M

2017-07-24

Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.