Science.gov

Sample records for accurate three-dimensional models

  1. A Flexible Fringe Projection Vision System with Extended Mathematical Model for Accurate Three-Dimensional Measurement

    PubMed Central

    Xiao, Suzhi; Tao, Wei; Zhao, Hui

    2016-01-01

    In order to acquire an accurate three-dimensional (3D) measurement, the traditional fringe projection technique applies complex and laborious procedures to compensate for the errors that exist in the vision system. However, the error sources in the vision system are very complex, such as lens distortion, lens defocus, and fringe pattern nonsinusoidality. Some errors cannot even be explained or rendered with clear expressions and are difficult to compensate directly as a result. In this paper, an approach is proposed that avoids the complex and laborious compensation procedure for error sources but still promises accurate 3D measurement. It is realized by the mathematical model extension technique. The parameters of the extended mathematical model for the ’phase to 3D coordinates transformation’ are derived using the least-squares parameter estimation algorithm. In addition, a phase-coding method based on a frequency analysis is proposed for the absolute phase map retrieval to spatially isolated objects. The results demonstrate the validity and the accuracy of the proposed flexible fringe projection vision system on spatially continuous and discontinuous objects for 3D measurement. PMID:27136553

  2. A Flexible Fringe Projection Vision System with Extended Mathematical Model for Accurate Three-Dimensional Measurement.

    PubMed

    Xiao, Suzhi; Tao, Wei; Zhao, Hui

    2016-01-01

    In order to acquire an accurate three-dimensional (3D) measurement, the traditional fringe projection technique applies complex and laborious procedures to compensate for the errors that exist in the vision system. However, the error sources in the vision system are very complex, such as lens distortion, lens defocus, and fringe pattern nonsinusoidality. Some errors cannot even be explained or rendered with clear expressions and are difficult to compensate directly as a result. In this paper, an approach is proposed that avoids the complex and laborious compensation procedure for error sources but still promises accurate 3D measurement. It is realized by the mathematical model extension technique. The parameters of the extended mathematical model for the 'phase to 3D coordinates transformation' are derived using the least-squares parameter estimation algorithm. In addition, a phase-coding method based on a frequency analysis is proposed for the absolute phase map retrieval to spatially isolated objects. The results demonstrate the validity and the accuracy of the proposed flexible fringe projection vision system on spatially continuous and discontinuous objects for 3D measurement. PMID:27136553

  3. Geo-accurate model extraction from three-dimensional image-derived point clouds

    NASA Astrophysics Data System (ADS)

    Nilosek, David; Sun, Shaohui; Salvaggio, Carl

    2012-06-01

    A methodology is proposed for automatically extracting primitive models of buildings in a scene from a three-dimensional point cloud derived from multi-view depth extraction techniques. By exploring the information provided by the two-dimensional images and the three-dimensional point cloud and the relationship between the two, automated methods for extraction are presented. Using the inertial measurement unit (IMU) and global positioning system (GPS) data that accompanies the aerial imagery, the geometry is derived in a world-coordinate system so the model can be used with GIS software. This work uses imagery collected by the Rochester Institute of Technology's Digital Imaging and Remote Sensing Laboratory's WASP sensor platform. The data used was collected over downtown Rochester, New York. Multiple target buildings have their primitive three-dimensional model geometry extracted using modern point-cloud processing techniques.

  4. TRIM—3D: a three-dimensional model for accurate simulation of shallow water flow

    USGS Publications Warehouse

    Casulli, Vincenzo; Bertolazzi, Enrico; Cheng, Ralph T.

    1993-01-01

    A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is discussed. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that the resulting algorithm permits the use of large time steps at a minimal computational cost. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers. The high computational efficiency of this method has made it possible to provide the fine details of circulation structure in complex regions that previous studies were unable to obtain. For proper interpretation of the model results suitable interactive graphics is also an essential tool.

  5. Validation of an Accurate Three-Dimensional Helical Slow-Wave Circuit Model

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1997-01-01

    The helical slow-wave circuit embodies a helical coil of rectangular tape supported in a metal barrel by dielectric support rods. Although the helix slow-wave circuit remains the mainstay of the traveling-wave tube (TWT) industry because of its exceptionally wide bandwidth, a full helical circuit, without significant dimensional approximations, has not been successfully modeled until now. Numerous attempts have been made to analyze the helical slow-wave circuit so that the performance could be accurately predicted without actually building it, but because of its complex geometry, many geometrical approximations became necessary rendering the previous models inaccurate. In the course of this research it has been demonstrated that using the simulation code, MAFIA, the helical structure can be modeled with actual tape width and thickness, dielectric support rod geometry and materials. To demonstrate the accuracy of the MAFIA model, the cold-test parameters including dispersion, on-axis interaction impedance and attenuation have been calculated for several helical TWT slow-wave circuits with a variety of support rod geometries including rectangular and T-shaped rods, as well as various support rod materials including isotropic, anisotropic and partially metal coated dielectrics. Compared with experimentally measured results, the agreement is excellent. With the accuracy of the MAFIA helical model validated, the code was used to investigate several conventional geometric approximations in an attempt to obtain the most computationally efficient model. Several simplifications were made to a standard model including replacing the helical tape with filaments, and replacing rectangular support rods with shapes conforming to the cylindrical coordinate system with effective permittivity. The approximate models are compared with the standard model in terms of cold-test characteristics and computational time. The model was also used to determine the sensitivity of various

  6. Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

    PubMed

    Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

    2014-07-01

    With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions.

  7. Three dimensional printing as an effective method of producing anatomically accurate models for studies in thermal ecology.

    PubMed

    Watson, Charles M; Francis, Gamal R

    2015-07-01

    Hollow copper models painted to match the reflectance of the animal subject are standard in thermal ecology research. While the copper electroplating process results in accurate models, it is relatively time consuming, uses caustic chemicals, and the models are often anatomically imprecise. Although the decreasing cost of 3D printing can potentially allow the reproduction of highly accurate models, the thermal performance of 3D printed models has not been evaluated. We compared the cost, accuracy, and performance of both copper and 3D printed lizard models and found that the performance of the models were statistically identical in both open and closed habitats. We also find that 3D models are more standard, lighter, durable, and inexpensive, than the copper electroformed models. PMID:25965016

  8. Three dimensional neuronal cell cultures more accurately model voltage gated calcium channel functionality in freshly dissected nerve tissue.

    PubMed

    Lai, Yinzhi; Cheng, Ke; Kisaalita, William

    2012-01-01

    It has been demonstrated that neuronal cells cultured on traditional flat surfaces may exhibit exaggerated voltage gated calcium channel (VGCC) functionality. To gain a better understanding of this phenomenon, primary neuronal cells harvested from mice superior cervical ganglion (SCG) were cultured on two dimensional (2D) flat surfaces and in three dimensional (3D) synthetic poly-L-lactic acid (PLLA) and polystyrene (PS) polymer scaffolds. These 2D- and 3D-cultured cells were compared to cells in freshly dissected SCG tissues, with respect to intracellular calcium increase in response to high K(+) depolarization. The calcium increases were identical for 3D-cultured and freshly dissected, but significantly higher for 2D-cultured cells. This finding established the physiological relevance of 3D-cultured cells. To shed light on the mechanism behind the exaggerated 2D-cultured cells' functionality, transcriptase expression and related membrane protein distributions (caveolin-1) were obtained. Our results support the view that exaggerated VGCC functionality from 2D cultured SCG cells is possibly due to differences in membrane architecture, characterized by uniquely organized caveolar lipid rafts. The practical implication of use of 3D-cultured cells in preclinical drug discovery studies is that such platforms would be more effective in eliminating false positive hits and as such improve the overall yield from screening campaigns.

  9. Accurate modeling and reconstruction of three-dimensional percolating filamentary microstructures from two-dimensional micrographs via dilation-erosion method

    SciTech Connect

    Guo, En-Yu; Chawla, Nikhilesh; Jing, Tao; Torquato, Salvatore; Jiao, Yang

    2014-03-01

    Heterogeneous materials are ubiquitous in nature and synthetic situations and have a wide range of important engineering applications. Accurate modeling and reconstructing three-dimensional (3D) microstructure of topologically complex materials from limited morphological information such as a two-dimensional (2D) micrograph is crucial to the assessment and prediction of effective material properties and performance under extreme conditions. Here, we extend a recently developed dilation–erosion method and employ the Yeong–Torquato stochastic reconstruction procedure to model and generate 3D austenitic–ferritic cast duplex stainless steel microstructure containing percolating filamentary ferrite phase from 2D optical micrographs of the material sample. Specifically, the ferrite phase is dilated to produce a modified target 2D microstructure and the resulting 3D reconstruction is eroded to recover the percolating ferrite filaments. The dilation–erosion reconstruction is compared with the actual 3D microstructure, obtained from serial sectioning (polishing), as well as the standard stochastic reconstructions incorporating topological connectedness information. The fact that the former can achieve the same level of accuracy as the latter suggests that the dilation–erosion procedure is tantamount to incorporating appreciably more topological and geometrical information into the reconstruction while being much more computationally efficient. - Highlights: • Spatial correlation functions used to characterize filamentary ferrite phase • Clustering information assessed from 3D experimental structure via serial sectioning • Stochastic reconstruction used to generate 3D virtual structure 2D micrograph • Dilation–erosion method to improve accuracy of 3D reconstruction.

  10. Three dimensional model of the human mandible.

    PubMed

    Muftić, O; Milcić, D; Saucha, J; Carek, V

    2000-07-01

    A new biomechanical three-dimensional (3D) model for the human mandible is proposed. A simple two-dimensional model cannot explain the biomechanics of the human mandible, where muscular forces through occlusion and condylar surfaces are in a state of dynamical 3D equilibrium. All forces are resolved into components according to a selected coordinate system. The muscular forces, which during clenching act on the jaw, along with the necessary force level for chewing, also act as some kind of stabilizers of the mandibular condyles preventing dislocation and loading of nonarticular tissues.

  11. Three-dimensional pancreas organogenesis models.

    PubMed

    Grapin-Botton, A

    2016-09-01

    A rediscovery of three-dimensional culture has led to the development of organ biogenesis, homeostasis and disease models applicable to human tissues. The so-called organoids that have recently flourished serve as valuable models bridging between cell lines or primary cells grown on the bottom of culture plates and experiments performed in vivo. Though not recapitulating all aspects of organ physiology, the miniature organs generated in a dish are useful models emerging for the pancreas, starting from embryonic progenitors, adult cells, tumour cells and stem cells. This review focusses on the currently available systems and their relevance to the study of the pancreas, of β-cells and of several pancreatic diseases including diabetes. We discuss the expected future developments for studying human pancreas development and function, for developing diabetes models and for producing therapeutic cells. PMID:27615129

  12. Three-dimensional model of lignin structure

    SciTech Connect

    Jurasek, L.

    1995-12-01

    An attempt to build a three-dimensional model of lignin structure using a computer program is described. The program simulates the biosynthesis of spruce lignin by allowing coniferyl alcohol subunits to be added randomly by six different types of linkages, assumed to be most common. The simulated biosynthesis starts from a number of seed points within restricted space, corresponding to 50 mM initial concentration of coniferyl alcohol. Rules of three-dimensional packing of the subunits within the lignin macro-molecule are observed during the simulated biosynthetic process. Branched oligomeric structures thus generated form crosslinks at those positions where the chains grow close enough to form a link. Inter-chain crosslinking usually joins the oligomers into one macromolecule. Intra-chain crosslinks are also formed and result in closed loops. Typically, a macromolecule with molecular weight of approx. 2 x 105 is formed, with internal density of 1.35g/cm3. Various characteristics of the internal structure, such as branching, crosslinking, bond frequencies, and chain length distribution are described. Breakdown of the polymer was also simulated and the effect of closed loops on the weight average molecular weight is shown. The effect of the shape of the biosynthetic space on the degree of crosslinking is discussed and predictions of the overall molecular shape of lignin particles are made.

  13. Multiscale modeling of three-dimensional genome

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Wolynes, Peter

    The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

  14. A three-dimensional human walking model

    NASA Astrophysics Data System (ADS)

    Yang, Q. S.; Qin, J. W.; Law, S. S.

    2015-11-01

    A three-dimensional human bipedal walking model with compliant legs is presented in this paper. The legs are modeled with time-variant dampers, and the model is able to characterize the gait pattern of an individual using a minimal set of parameters. Feedback control, for both the forward and lateral movements, is implemented to regulate the walking performance of the pedestrian. The model provides an improvement over classic invert pendulum models. Numerical studies were undertaken to investigate the effects of leg stiffness and attack angle. Simulation results show that when walking at a given speed, increasing the leg stiffness with a constant attack angle results in a longer step length, a higher step frequency, a faster walking speed and an increase in both the peak vertical and lateral ground reaction forces. Increasing the attack angle with a constant leg stiffness results in a higher step frequency, a decrease in the step length, an increase in the total energy of the system and a decrease in both the peak vertical and lateral ground reaction forces.

  15. An Accurate von Neumann's Law for Three-Dimensional Foams

    SciTech Connect

    Hilgenfeldt, Sascha; Kraynik, Andrew M.; Koehler, Stephan A.; Stone, Howard A.

    2001-03-19

    The diffusive coarsening of 2D soap froths is governed by von Neumann's law. A statistical version of this law for dry 3D foams has long been conjectured. A new derivation, based on a theorem by Minkowski, yields an explicit analytical von Neumann's law in 3D which is in very good agreement with detailed simulations and experiments. The average growth rate of a bubble with F faces is shown to be proportional to F{sup 1/2} for large F , in contrast to the conjectured linear dependence. Accounting for foam disorder in the model further improves the agreement with data.

  16. Three-dimensional modeling of tsunami waves

    SciTech Connect

    Mader, C.L.

    1985-01-01

    Two- and three-dimensional, time-dependent, nonlinear, incompressible, viscous flow calculations of realistic models of tsunami wave formation and run up have been performed using the Los Alamos-developed SOLA-3D code. The results of the SOLA calculations are compared with shallow-water, long-wave calculations for the same problems using the SWAN code. Tsunami wave formation by a continental slope subsidence has been examined using the two numerical models. The SOLA waves were slower than the SWAN waves and the interaction with the shoreline was more complicated for the SOLA waves. In the SOLA calculation, the first wave was generated by the cavity being filled along the shoreline close to the source of motion. The second wave was generated by the cavity being filled from the deep water end. The two waves interacted along the shoreline resulting in the second wave being the largest wave with a velocity greater than the first wave. The second wave overtook the first wave at later times and greater distances from the source. In the SWAN calculation, the second wave was smaller than the first wave. 6 refs.

  17. Three-dimensional ring current decay model

    NASA Astrophysics Data System (ADS)

    Fok, Mei Ching; Moore, Thomas E.; Kozyra, Janet U.; Ho, George C.; Hamilton, Douglas C.

    1995-06-01

    This work is an extension of a previous ring current decay model. In the previous work, a two-dimensional kinetic model was constructed to study the temporal variations of the equatorially mirroring ring current ions, considering charge exchange and Coulomb drag losses along drift paths in a magnetic dipole field. In this work, particles with arbitrary pitch angle are considered. By bounce averaging the kinetic equation of the phase space density, information along magnetic field lines can be inferred from the equator. The three-dimensional model is used to simulate the recovery phase of a model great magnetic storm, similar to that which occurred in early February 1986. The initial distribution of ring current ions (at the minimum Dst) is extrapolated to all local times from AMPTE/CCE spacecraft observations on the dawnside and duskside of the inner magnetosphere spanning the L value range L=2.25 to 6.75. Observations by AMPTE/CCE of ring current distributions over subsequent orbits during the storm recovery phase are compared to model outputs. In general, the calculated ion fluxes are consistent with observations, except for H+ fluxes at tens of keV, which are always overestimated. A newly invented visualization idea, designated as a chromogram, is used to display the spatial and energy dependence of the ring current ion diifferential flux. Important features of storm time ring current, such as day-night asymmetry during injection and drift hole on the dayside at low energies (<10 keV), are manifested in the chromogram representation. The pitch angle distribution is well fit by the function, j0(1+Ayn), where y is sine of the equatorial pitch angle. The evolution of the index n is a combined effect of charge exchange loss and particle drift. At low energies (<30 keV), both drift dispersion and charge exchange are important in determining n. ©American Geophysical 1995

  18. Three-dimensional ring current decay model

    NASA Technical Reports Server (NTRS)

    Fok, Mei-Ching; Moore, Thomas E.; Kozyra, Janet U.; Ho, George C.; Hamilton, Douglas C.

    1995-01-01

    This work is an extension of a previous ring current decay model. In the previous work, a two-dimensional kinetic model was constructed to study the temporal variations of the equatorially mirroring ring current ions, considering charge exchange and Coulomb drag losses along drift paths in a magnetic dipole field. In this work, particles with arbitrary pitch angle are considered. By bounce averaging the kinetic equation of the phase space density, information along magnetic field lines can be inferred from the equator. The three-dimensional model is used to simulate the recovery phase of a model great magnetic storm, similar to that which occurred in early February 1986. The initial distribution of ring current ions (at the minimum Dst) is extrapolated to all local times from AMPTE/CCE spacecraft observations on the dawnside and duskside of the inner magnetosphere spanning the L value range L = 2.25 to 6.75. Observations by AMPTE/CCE of ring current distributions over subsequent orbits during the storm recovery phase are compared to model outputs. In general, the calculated ion fluxes are consistent with observations, except for H(+) fluxes at tens of keV, which are always overestimated. A newly invented visualization idea, designated as a chromogram, is used to display the spatial and energy dependence of the ring current ion differential flux. Important features of storm time ring current, such as day-night asymmetry during injection and drift hole on the dayside at low energies (less than 10 keV), are manifested in the chromogram representation. The pitch angle distribution is well fit by the function, J(sub o)(1 + Ay(sup n)), where y is sine of the equatorial pitch angle. The evolution of the index n is a combined effect of charge exchange loss and particle drift. At low energies (less than 30 keV), both drift dispersion and charge exchange are important in determining n.

  19. Three dimensional modelling of ICRF launchers for fusion devices

    NASA Astrophysics Data System (ADS)

    Carter, M. D.; Rasmussen, D. A.; Ryan, P. M.; Hanson, G. R.; Stallings, D. C.; Batchelor, D. B.; Bigelow, T. S.; England, A. C.; Hoffman, D. J.; Murakami, M.; Wang, C. Y.; Wilgen, J. B.; Rogers, J. H.; Wilson, J. R.; Majeski, R.; Schilling, G.

    1996-02-01

    The three dimensional (3-D) nature of antennas for fusion applications in the ion cyclotron range of frequencies (ICRF) requires accurate modelling to design and analyse new antennas. In this article, analysis and design tools for radiofrequency (RF) antennas are successfully benchmarked with experiment, and the 3-D physics of the launched waves is explored. The systematic analysis combines measured density profiles from a reflectometer system, transmission line circuit modelling, detailed 3-D magnetostatics modelling and a new 3-D electromagnetic antenna model including plasma. This analysis gives very good agreement with measured loading data from the Tokamak Fusion Test Reactor (TFTR) Bay-M antenna, thus demonstrating the validity of the analysis for the design of new RF antennas. The 3-D modelling is contrasted with 2-D models, and significant deficiencies are found in the latter. The 2-D models are in error by as much as a factor of 2 in real and reactive loading, even after they are corrected for the most obvious 3-D effects. Three dimensional effects play the most significant role at low parallel wavenumbers, where the launched power spectrum can be quite different from the predictions of 2-D models. Three dimensional effects should not be ignored for many RF designs, especially those intended for fast wave current drive

  20. Accurate color synthesis of three-dimensional objects in an image

    NASA Astrophysics Data System (ADS)

    Xin, John H.; Shen, Hui-Liang

    2004-05-01

    Our study deals with color synthesis of a three-dimensional object in an image; i.e., given a single image, a target color can be accurately mapped onto the object such that the color appearance of the synthesized object closely resembles that of the actual one. As it is almost impossible to acquire the complete geometric description of the surfaces of an object in an image, this study attempted to recover the implicit description of geometry for the color synthesis. The description was obtained from either a series of spectral reflectances or the RGB signals at different surface positions on the basis of the dichromatic reflection model. The experimental results showed that this implicit image-based representation is related to the object geometry and is sufficient for accurate color synthesis of three-dimensional objects in an image. The method established is applicable to the color synthesis of both rigid and deformable objects and should contribute to color fidelity in virtual design, manufacturing, and retailing.

  1. Accurate color synthesis of three-dimensional objects in an image.

    PubMed

    Xin, John H; Shen, Hui-Liang

    2004-05-01

    Our study deals with color synthesis of a three-dimensional object in an image; i.e., given a single image, a target color can be accurately mapped onto the object such that the color appearance of the synthesized object closely resembles that of the actual one. As it is almost impossible to acquire the complete geometric description of the surfaces of an object in an image, this study attempted to recover the implicit description of geometry for the color synthesis. The description was obtained from either a series of spectral reflectances or the RGB signals at different surface positions on the basis of the dichromatic reflection model. The experimental results showed that this implicit image-based representation is related to the object geometry and is sufficient for accurate color synthesis of three-dimensional objects in an image. The method established is applicable to the color synthesis of both rigid and deformable objects and should contribute to color fidelity in virtual design, manufacturing, and retailing. PMID:15139423

  2. Accurate three-dimensional pose recognition from monocular images using template matched filtering

    NASA Astrophysics Data System (ADS)

    Picos, Kenia; Diaz-Ramirez, Victor H.; Kober, Vitaly; Montemayor, Antonio S.; Pantrigo, Juan J.

    2016-06-01

    An accurate algorithm for three-dimensional (3-D) pose recognition of a rigid object is presented. The algorithm is based on adaptive template matched filtering and local search optimization. When a scene image is captured, a bank of correlation filters is constructed to find the best correspondence between the current view of the target in the scene and a target image synthesized by means of computer graphics. The synthetic image is created using a known 3-D model of the target and an iterative procedure based on local search. Computer simulation results obtained with the proposed algorithm in synthetic and real-life scenes are presented and discussed in terms of accuracy of pose recognition in the presence of noise, cluttered background, and occlusion. Experimental results show that our proposal presents high accuracy for 3-D pose estimation using monocular images.

  3. The crystallization of biological macromolecules under microgravity: a way to more accurate three-dimensional structures?

    PubMed

    Lorber, Bernard

    2002-09-23

    The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.

  4. Modeling of Unsteady Three-dimensional Flows in Multistage Machines

    NASA Technical Reports Server (NTRS)

    Hall, Kenneth C.; Pratt, Edmund T., Jr.; Kurkov, Anatole (Technical Monitor)

    2003-01-01

    Despite many years of development, the accurate and reliable prediction of unsteady aerodynamic forces acting on turbomachinery blades remains less than satisfactory, especially when viewed next to the great success investigators have had in predicting steady flows. Hall and Silkowski (1997) have proposed that one of the main reasons for the discrepancy between theory and experiment and/or industrial experience is that many of the current unsteady aerodynamic theories model a single blade row in an infinitely long duct, ignoring potentially important multistage effects. However, unsteady flows are made up of acoustic, vortical, and entropic waves. These waves provide a mechanism for the rotors and stators of multistage machines to communicate with one another. In other words, wave behavior makes unsteady flows fundamentally a multistage (and three-dimensional) phenomenon. In this research program, we have has as goals (1) the development of computationally efficient computer models of the unsteady aerodynamic response of blade rows embedded in a multistage machine (these models will ultimately be capable of analyzing three-dimensional viscous transonic flows), and (2) the use of these computer codes to study a number of important multistage phenomena.

  5. Three-Dimensional Lithium-Ion Battery Model (Presentation)

    SciTech Connect

    Kim, G. H.; Smith, K.

    2008-05-01

    Nonuniform battery physics can cause unexpected performance and life degradations in lithium-ion batteries; a three-dimensional cell performance model was developed by integrating an electrode-scale submodel using a multiscale modeling scheme.

  6. Bootstrapping Critical Ising Model on Three Dimensional Real Projective Space.

    PubMed

    Nakayama, Yu

    2016-04-01

    Given conformal data on a flat Euclidean space, we use crosscap conformal bootstrap equations to numerically solve the Lee-Yang model as well as the critical Ising model on a three dimensional real projective space. We check the rapid convergence of our bootstrap program in two dimensions from the exact solutions available. Based on the comparison, we estimate that our systematic error on the numerically solved one-point functions of the critical Ising model on a three dimensional real projective space is less than 1%. Our method opens up a novel way to solve conformal field theories on nontrivial geometries.

  7. Three-dimensional modeling of the plasma arc in arc welding

    SciTech Connect

    Xu, G.; Tsai, H. L.; Hu, J.

    2008-11-15

    Most previous three-dimensional modeling on gas tungsten arc welding (GTAW) and gas metal arc welding (GMAW) focuses on the weld pool dynamics and assumes the two-dimensional axisymmetric Gaussian distributions for plasma arc pressure and heat flux. In this article, a three-dimensional plasma arc model is developed, and the distributions of velocity, pressure, temperature, current density, and magnetic field of the plasma arc are calculated by solving the conservation equations of mass, momentum, and energy, as well as part of the Maxwell's equations. This three-dimensional model can be used to study the nonaxisymmetric plasma arc caused by external perturbations such as an external magnetic field. It also provides more accurate boundary conditions when modeling the weld pool dynamics. The present work lays a foundation for true three-dimensional comprehensive modeling of GTAW and GMAW including the plasma arc, weld pool, and/or electrode.

  8. Interactive Multimedia and Concrete Three-Dimensional Modelling.

    ERIC Educational Resources Information Center

    Baxter, J. H.; Preece, Peter F. W.

    1999-01-01

    Compares a multimedia package for teaching about the phases of the moon to grade 8 (12-year-old) students with a conventional three-dimensional modeling approach. Results show both methods were equally effective in terms of student learning, for male and female students, and prior computer experience was not a factor in multimedia use. (Author/LRW)

  9. THREE-DIMENSIONAL NAPL FATE AND TRANSPORT MODEL

    EPA Science Inventory

    We have added several new and significant capabilities to UTCHEM to make it into a general-purpose NAPL simulator. The simulator is now capable of modeling transient and steady-state three-dimensional flow and mass transport in the groundwater (saturated) and vadose (unsaturated...

  10. Revisit to three-dimensional percolation theory: Accurate analysis for highly stretchable conductive composite materials

    PubMed Central

    Kim, Sangwoo; Choi, Seongdae; Oh, Eunho; Byun, Junghwan; Kim, Hyunjong; Lee, Byeongmoon; Lee, Seunghwan; Hong, Yongtaek

    2016-01-01

    A percolation theory based on variation of conductive filler fraction has been widely used to explain the behavior of conductive composite materials under both small and large deformation conditions. However, it typically fails in properly analyzing the materials under the large deformation since the assumption may not be valid in such a case. Therefore, we proposed a new three-dimensional percolation theory by considering three key factors: nonlinear elasticity, precisely measured strain-dependent Poisson’s ratio, and strain-dependent percolation threshold. Digital image correlation (DIC) method was used to determine actual Poisson’s ratios at various strain levels, which were used to accurately estimate variation of conductive filler volume fraction under deformation. We also adopted strain-dependent percolation threshold caused by the filler re-location with deformation. When three key factors were considered, electrical performance change was accurately analyzed for composite materials with both isotropic and anisotropic mechanical properties. PMID:27694856

  11. Recent developments in three-dimensional numerical estuarine models

    USGS Publications Warehouse

    Cheng, Ralph T.; Smith, Peter E.; Casulli, Vincenzo

    1993-01-01

    For a fixed cost, computing power increases 5 to 10 times every five years. The readily available computing resources have inspired new modal formulations and innovative model applications. Significant progress has been advanced in three-dimensional numerical estuarine modeling within the past three or four years. This paper attempts to review and summarize properties of new 3-D estuarine hydrodynamic models. The emphasis of the review is placed on the formulation, numerical methods. The emphasis of the review is placed on the formulation, numerical methods, spatial and temporal resolution, computational efficiency, and turbulence closure of new models. Recent research has provided guidelines for the proper use of 3-D models involving in the σ-transformation. Other models resort to a fixed level discretization in the vertical. The semi-implicit treatment in time-stepping models appears to have gained momentum. Future research in three-dimensional numerical modeling remains to be on computational efficiency and turbulent closure.

  12. Three-dimensional models. [For orbital celestial mechanics

    SciTech Connect

    Hunter, C. )

    1990-06-01

    The Schwarzschild (1979) approach to the analysis of three-dimensional galactic models is reviewed. An analysis of triaxial Staeckel models is discussed which shows that such models have a wide variety of possible distribution functions. The uniqueness that Schwarzschild first encountered in his discrete formulation of the problem of finding a three-integral distribution function for a triaxial density is real and not an artifact of the finite cell approximation. 27 refs.

  13. A time accurate finite volume high resolution scheme for three dimensional Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Liou, Meng-Sing; Hsu, Andrew T.

    1989-01-01

    A time accurate, three-dimensional, finite volume, high resolution scheme for solving the compressible full Navier-Stokes equations is presented. The present derivation is based on the upwind split formulas, specifically with the application of Roe's (1981) flux difference splitting. A high-order accurate (up to the third order) upwind interpolation formula for the inviscid terms is derived to account for nonuniform meshes. For the viscous terms, discretizations consistent with the finite volume concept are described. A variant of second-order time accurate method is proposed that utilizes identical procedures in both the predictor and corrector steps. Avoiding the definition of midpoint gives a consistent and easy procedure, in the framework of finite volume discretization, for treating viscous transport terms in the curvilinear coordinates. For the boundary cells, a new treatment is introduced that not only avoids the use of 'ghost cells' and the associated problems, but also satisfies the tangency conditions exactly and allows easy definition of viscous transport terms at the first interface next to the boundary cells. Numerical tests of steady and unsteady high speed flows show that the present scheme gives accurate solutions.

  14. Three Dimensional Thermal Abuse Reaction Model for Lithium Ion Batteries

    2006-06-29

    Three dimensional computer models for simulating thermal runaway of lithium ion battery was developed. The three-dimensional model captures the shapes and dimensions of cell components and the spatial distributions of materials and temperatures, so we could consider the geometrical features, which are critical especially in large cells. An array of possible exothermic reactions, such as solid-electrolyte-interface (SEI) layer decomposition, negative active/electrolyte reaction, and positive active/electrolyte reaction, were considered and formulated to fit experimental data frommore » accelerating rate calorimetry and differential scanning calorimetry. User subroutine code was written to implement NREL developed approach and to utilize a commercially available solver. The model is proposed to use for simulation a variety of lithium-ion battery safety events including thermal heating and short circuit.« less

  15. Three-dimensional radiation transfer modeling in a dicotyledon leaf

    NASA Astrophysics Data System (ADS)

    Govaerts, Yves M.; Jacquemoud, Stéphane; Verstraete, Michel M.; Ustin, Susan L.

    1996-11-01

    The propagation of light in a typical dicotyledon leaf is investigated with a new Monte Carlo ray-tracing model. The three-dimensional internal cellular structure of the various leaf tissues, including the epidermis, the palisade parenchyma, and the spongy mesophyll, is explicitly described. Cells of different tissues are assigned appropriate morphologies and contain realistic amounts of water and chlorophyll. Each cell constituent is characterized by an index of refraction and an absorption coefficient. The objective of this study is to investigate how the internal three-dimensional structure of the tissues and the optical properties of cell constituents control the reflectance and transmittance of the leaf. Model results compare favorably with laboratory observations. The influence of the roughness of the epidermis on the reflection and absorption of light is investigated, and simulation results confirm that convex cells in the epidermis focus light on the palisade parenchyma and increase the absorption of radiation.

  16. Towards Accurate Prediction of Turbulent, Three-Dimensional, Recirculating Flows with the NCC

    NASA Technical Reports Server (NTRS)

    Iannetti, A.; Tacina, R.; Jeng, S.-M.; Cai, J.

    2001-01-01

    The National Combustion Code (NCC) was used to calculate the steady state, nonreacting flow field of a prototype Lean Direct Injection (LDI) swirler. This configuration used nine groups of eight holes drilled at a thirty-five degree angle to induce swirl. These nine groups created swirl in the same direction, or a corotating pattern. The static pressure drop across the holes was fixed at approximately four percent. Computations were performed on one quarter of the geometry, because the geometry is considered rotationally periodic every ninety degrees. The final computational grid used was approximately 2.26 million tetrahedral cells, and a cubic nonlinear k - epsilon model was used to model turbulence. The NCC results were then compared to time averaged Laser Doppler Velocimetry (LDV) data. The LDV measurements were performed on the full geometry, but four ninths of the geometry was measured. One-, two-, and three-dimensional representations of both flow fields are presented. The NCC computations compare both qualitatively and quantitatively well to the LDV data, but differences exist downstream. The comparison is encouraging, and shows that NCC can be used for future injector design studies. To improve the flow prediction accuracy of turbulent, three-dimensional, recirculating flow fields with the NCC, recommendations are given.

  17. Three dimensional global modeling of atmospheric CO2

    NASA Technical Reports Server (NTRS)

    Fung, I.; Hansen, J.; Rind, D.

    1983-01-01

    A model was developed to study the prospects of extracting information on carbon dioxide sources and sinks from observed CO2 variations. The approach uses a three dimensional global transport model, based on winds from a 3-D general circulation model (GCM), to advect CO2 noninteractively, i.e., as a tracer, with specified sources and sinks of CO2 at the surface. The 3-D model employed is identified and biosphere, ocean and fossil fuel sources and sinks are discussed. Some preliminary model results are presented.

  18. Three-dimensional Physical Modeling: Applications and Experience at Mayo Clinic.

    PubMed

    Matsumoto, Jane S; Morris, Jonathan M; Foley, Thomas A; Williamson, Eric E; Leng, Shuai; McGee, Kiaran P; Kuhlmann, Joel L; Nesberg, Linda E; Vrtiska, Terri J

    2015-01-01

    Radiologists will be at the center of the rapid technologic expansion of three-dimensional (3D) printing of medical models, as accurate models depend on well-planned, high-quality imaging studies. This article outlines the available technology and the processes necessary to create 3D models from the radiologist's perspective. We review the published medical literature regarding the use of 3D models in various surgical practices and share our experience in creating a hospital-based three-dimensional printing laboratory to aid in the planning of complex surgeries.

  19. Three-dimensional "Mercedes-Benz" model for water.

    PubMed

    Dias, Cristiano L; Ala-Nissila, Tapio; Grant, Martin; Karttunen, Mikko

    2009-08-01

    In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: The anomalous density profile, the negative thermal expansivity, the large heat capacity, and the minimum in the isothermal compressibility.

  20. Three-dimensional ``Mercedes-Benz'' model for water

    NASA Astrophysics Data System (ADS)

    Dias, Cristiano L.; Ala-Nissila, Tapio; Grant, Martin; Karttunen, Mikko

    2009-08-01

    In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: The anomalous density profile, the negative thermal expansivity, the large heat capacity, and the minimum in the isothermal compressibility.

  1. Three-dimensional "Mercedes-Benz" model for water.

    PubMed

    Dias, Cristiano L; Ala-Nissila, Tapio; Grant, Martin; Karttunen, Mikko

    2009-08-01

    In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: The anomalous density profile, the negative thermal expansivity, the large heat capacity, and the minimum in the isothermal compressibility. PMID:19673572

  2. Spatial clustering method based on three-dimensional cloud model

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Wang, Li; Deng, Yu; Liu, Jia

    2008-12-01

    Spatial clustering is one of those major methods applying to spatial data mining and knowledge discovery. The purpose of this paper is to set forth Spatial Clustering Method Based on Multidimensional Cloud Model, which can be widely applied to the research on classification and hierarchy in realm of spatial data mining and knowledge discovery. This paper summarizes all kinds of cloud model and analyzes the optimalizing form of spatial data-three-dimensional cloud model. The limitation which sets the weighing value subjectively in traditional way and propagation of error can be avoided. The implementation procedure of this method is advanced, and the feasibility of this method is proven through experiments effectively.

  3. Three Dimensional Vapor Intrusion Modeling: Model Validation and Uncertainty Analysis

    NASA Astrophysics Data System (ADS)

    Akbariyeh, S.; Patterson, B.; Rakoczy, A.; Li, Y.

    2013-12-01

    Volatile organic chemicals (VOCs), such as chlorinated solvents and petroleum hydrocarbons, are prevalent groundwater contaminants due to their improper disposal and accidental spillage. In addition to contaminating groundwater, VOCs may partition into the overlying vadose zone and enter buildings through gaps and cracks in foundation slabs or basement walls, a process termed vapor intrusion. Vapor intrusion of VOCs has been recognized as a detrimental source for human exposures to potential carcinogenic or toxic compounds. The simulation of vapor intrusion from a subsurface source has been the focus of many studies to better understand the process and guide field investigation. While multiple analytical and numerical models were developed to simulate the vapor intrusion process, detailed validation of these models against well controlled experiments is still lacking, due to the complexity and uncertainties associated with site characterization and soil gas flux and indoor air concentration measurement. In this work, we present an effort to validate a three-dimensional vapor intrusion model based on a well-controlled experimental quantification of the vapor intrusion pathways into a slab-on-ground building under varying environmental conditions. Finally, a probabilistic approach based on Monte Carlo simulations is implemented to determine the probability distribution of indoor air concentration based on the most uncertain input parameters.

  4. An algebraic turbulence model for three-dimensional viscous flows

    NASA Technical Reports Server (NTRS)

    Chima, R. V.; Giel, P. W.; Boyle, R. J.

    1993-01-01

    An algebraic turbulence model is proposed for use with three-dimensional Navier-Stokes analyses. It incorporates features of both the Baldwin-Lomax and Cebeci-Smith models. The Baldwin-Lomax model uses the maximum of a function f(y) to determine length and velocity scales. An analysis of the Baldwin-Lomax model shows that f(y) can have a spurious maximum close to the wall, causing numerical problems and non-physical results. The proposed model uses integral relations to determine delta(*) u(sub e) and delta used in the Cebeci-Smith mode. It eliminates a constant in the Baldwin-Lomax model and determines the two remaining constants by comparison to the Cebeci-Smith formulation. Pressure gradient effects, a new wake model, and the implementation of these features in a three-dimensional Navier-Stokes code are also described. Results are shown for a flat plate boundary layer, an annular turbine cascade, and endwall heat transfer in a linear turbine cascade. The heat transfer results agree well with experimental data which shows large variations in endwall Stanton number contours with Reynolds number.

  5. A three-dimensional spin-diffusion model for micromagnetics

    NASA Astrophysics Data System (ADS)

    Abert, Claas; Ruggeri, Michele; Bruckner, Florian; Vogler, Christoph; Hrkac, Gino; Praetorius, Dirk; Suess, Dieter

    2015-10-01

    We solve a time-dependent three-dimensional spin-diffusion model coupled to the Landau-Lifshitz-Gilbert equation numerically. The presented model is validated by comparison to two established spin-torque models: The model of Slonzewski that describes spin-torque in multi-layer structures in the presence of a fixed layer and the model of Zhang and Li that describes current driven domain-wall motion. It is shown that both models are incorporated by the spin-diffusion description, i.e., the nonlocal effects of the Slonzewski model are captured as well as the spin-accumulation due to magnetization gradients as described by the model of Zhang and Li. Moreover, the presented method is able to resolve the time dependency of the spin-accumulation.

  6. A three-dimensional spin-diffusion model for micromagnetics

    PubMed Central

    Abert, Claas; Ruggeri, Michele; Bruckner, Florian; Vogler, Christoph; Hrkac, Gino; Praetorius, Dirk; Suess, Dieter

    2015-01-01

    We solve a time-dependent three-dimensional spin-diffusion model coupled to the Landau-Lifshitz-Gilbert equation numerically. The presented model is validated by comparison to two established spin-torque models: The model of Slonzewski that describes spin-torque in multi-layer structures in the presence of a fixed layer and the model of Zhang and Li that describes current driven domain-wall motion. It is shown that both models are incorporated by the spin-diffusion description, i.e., the nonlocal effects of the Slonzewski model are captured as well as the spin-accumulation due to magnetization gradients as described by the model of Zhang and Li. Moreover, the presented method is able to resolve the time dependency of the spin-accumulation. PMID:26442796

  7. Three dimensional model for surgical planning in resection of thoracic tumors

    PubMed Central

    Kim, Min P.; Ta, Anderson H.; Ellsworth, Warren A.; Marco, Rex A.; Gaur, Puja; Miller​, Jordan S.

    2015-01-01

    Introduction The computed tomography scan provides vital information about the relationship of thoracic malignancies to the surrounding structures and aids in surgical planning. However, it can be difficult to visualize the images in a two-dimensional screen to interpret the full extent of the relationship between important structures in the surgical field. Presentation of case We report two cases where we used a three-dimensional printed model to aid in the surgical resection of thoracic malignancies. Discussion Careful planning is necessary to resect thoracic malignancies. Although two-dimensional images of the thoracic malignancies provide vital information about the tumor and its surrounding structures, the three-dimensional printed model can provide more accurate information about the tumor and assist in surgical planning. Conclusion Three-dimensional printed model provide better visualization of complex thoracic tumors, aid in counseling the patient about the surgical procedure and assisted in surgical resection of thoracic malignancy. PMID:26453940

  8. Accurate quantum thermal rate constants for the three-dimensional H+H2 reaction

    NASA Astrophysics Data System (ADS)

    Park, Tae Jun; Light, J. C.

    1989-07-01

    The rate constants for the three-dimensional H+H2 reaction on the Liu-Siegbahn-Truhlar-Horowitz (LSTH) surface are calculated using Pack-Parker hyperspherical (APH) coordinates and a C2v symmetry adapted direct product discrete variable representation (DVR). The C2v symmetry decomposition and the parity decoupling on the basis are performed for the internal coordinate χ. The symmetry decomposition results in a block diagonal representation of the flux and Hamiltonian operators. The multisurface flux is introduced to represent the multichannel reactive flux. The eigenvalues and eigenvectors of the J=0 internal Hamiltonian are obtained by sequential diagonalization and truncation. The individual symmetry blocks of the flux operator are propagated by the corresponding blocks of the Hamiltonian, and the J=0 rate constant k0(T) is obtained as a sum of the rate constants calculated for each block. k0(T) is compared with the exact k0(T) obtained from thermal averaging of the J=0 reaction probabilities; the errors are within 5%-20% up to T=1500 K. The sequential diagonalization-truncation method reduces the size of the Hamiltonian greatly, but the resulting Hamiltonian matrix still describes the time evolution very accurately. For the J≠0 rate constant calculations, the truncated internal Hamiltonian eigenvector basis is used to construct reduced (JKJ) blocks of the Hamiltonian. The individual (JKJ) blocks are diagonalized neglecting Coriolis coupling and treating the off-diagonal KJ±2 couplings by second order perturbation theory. The full wave function is parity decoupled. The rate constant is obtained as a sum over J of (2J+1)kJ(T). The time evolution of the flux for J≠0 is again very accurately described to give a well converged rate constant.

  9. On multiscale approaches to three-dimensional modelling of morphogenesis

    PubMed Central

    Chaturvedi, R; Huang, C; Kazmierczak, B; Schneider, T; Izaguirre, J.A; Glimm, T; Hentschel, H.G.E; Glazier, J.A; Newman, S.A; Alber, M.S

    2005-01-01

    In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction–diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb. PMID:16849182

  10. Three-dimensional numerical model for soil vapor extraction.

    PubMed

    Nguyen, Van Thinh; Zhao, Lian; Zytner, Richard G

    2013-04-01

    Mass transfer limitations impact the effectiveness of soil vapor extraction (SVE) and cause tailing. In order to identify the governing mass transfer processes, a three-dimensional SVE numerical model was developed. The developed model was based on Comsol Multiphysics a finite element method that incorporates multi-phase flow, multi-component transport and non-equilibrium transient mass transfer. Model calibration was done against experimental data from previously completed lab-scale reactor experiments. The developed model, 3D-SVE, nicely simulates laboratory findings and allows for changes in the important governing mass transfer relationships. The modeling results showed that a single averaged mass transfer value is a poor representation of the entire SVE operation, and that a transient mass transfer coefficient is required to fully represent SVE tailing. Calibration of the lab scale model showed that the most important mass transfer occurs between the NAPL and vapor phase.

  11. Three-dimensional thermochemical nonequilibrium flow modeling for hypersonic flows

    NASA Technical Reports Server (NTRS)

    Tam, L. T.; Li, C. P.

    1989-01-01

    A three-dimensional thermochemical nonequilibrium model has been developed and applied to the study of entry flows surrounding space vehicles. The model accounts for both chemical and vibrational nonequilibrium phenomena behind the bow shock. The thermodynamic state of a real gas is modeled with a translational-rotational temperature and a electron-vibrational temperature. Their internal energies are averaged to determine the temperature used in the reaction rates calculation. In order to establish the validity of the selected models, both one- and two-temperature models with seven and/or eleven species were investigated. Several numerical experiments that include a sphere, the RAMC vehicle and 3D AFE forebody flows were performed. Preliminary results were compared with RAMC-II experimental data. Good agreement was obtained after a two-temperature model with eleven species and thirty reactions was incorporated into the study.

  12. Three Dimensional Modeling of an MRI Actuated Steerable Catheter System.

    PubMed

    Liu, Taoming; Cavuşoğlu, M Cenk

    2014-01-01

    This paper presents the three dimensional kinematic modeling of a novel steerable robotic ablation catheter system. The catheter, embedded with a set of current-carrying micro-coils, is actuated by the magnetic forces generated by the magnetic field of the MRI scanner. This paper develops a 3D model of the MRI actuated steerable catheter system by using finite differences approach. For each finite segment, a quasi-static torque-deflection equilibrium equation is calculated using beam theory. By using the deflection displacements and torsion angles, the kinematic modeling of the catheter system is derived. The proposed models are evaluated by comparing the simulation results of the proposed model with the experimental results of a proof-of-concept prototype. PMID:25328804

  13. Three-dimensional face model reproduction method using multiview images

    NASA Astrophysics Data System (ADS)

    Nagashima, Yoshio; Agawa, Hiroshi; Kishino, Fumio

    1991-11-01

    This paper describes a method of reproducing three-dimensional face models using multi-view images for a virtual space teleconferencing system that achieves a realistic visual presence for teleconferencing. The goal of this research, as an integral component of a virtual space teleconferencing system, is to generate a three-dimensional face model from facial images, synthesize images of the model virtually viewed from different angles, and with natural shadow to suit the lighting conditions of the virtual space. The proposed method is as follows: first, front and side view images of the human face are taken by TV cameras. The 3D data of facial feature points are obtained from front- and side-views by an image processing technique based on the color, shape, and correlation of face components. Using these 3D data, the prepared base face models, representing typical Japanese male and female faces, are modified to approximate the input facial image. The personal face model, representing the individual character, is then reproduced. Next, an oblique view image is taken by TV camera. The feature points of the oblique view image are extracted using the same image processing technique. A more precise personal model is reproduced by fitting the boundary of the personal face model to the boundary of the oblique view image. The modified boundary of the personal face model is determined by using face direction, namely rotation angle, which is detected based on the extracted feature points. After the 3D model is established, the new images are synthesized by mapping facial texture onto the model.

  14. Star-triangle relation for a three-dimensional model

    SciTech Connect

    Bazhanov, V.V. Institute for High Eenrgy Physics, Protvino, Moscow Region ); Baxter, R.J. Australian National Univ., Canberra )

    1993-06-01

    The solvable sl(n)-chiral Potts model can be interpreted as a three-dimensional lattice model with local interactions. To within a minor modification of the boundary conditions it is an Ising-type model on the body-centered cubic lattice with two- and three-spin interactions. The corresponding local Boltzmann weights obey a number of simple relations, including a restricted star-triangle relation, which is a modified version of the well-known star-triangle relation appearing in two-dimensional models. It is shown that these relations lead to remarkable symmetry properties of the Boltzmann weight function of an elementary cube of the lattice, related to the spatial symmetry group of the cubic lattice. These symmetry properties allow one to prove the commutativity of the row-to-row transfer matrices, bypassing the tetrahedron relation. The partition function per site for the infinite lattice is calculated exactly. 20 refs., 4 figs.

  15. Three-dimensional Myoblast Aggregates--Effects of Modeled Microgravity

    NASA Technical Reports Server (NTRS)

    Byerly, Diane; Sognier, M. A.; Marquette, M. L.

    2006-01-01

    The overall objective of these studies is to elucidate the molecular and cellular alterations that contribute to muscle atrophy in astronauts caused by exposure to microgravity conditions in space. To accomplish this, a three-dimensional model test system was developed using mouse myoblast cells (C2C12). Myoblast cells were grown as three-dimensional aggregates (without scaffolding or other solid support structures) in both modeled microgravity (Rotary Cell Culture System, Synthecon, Inc.) and at unit gravity in coated Petri dishes. Evaluation of H&E stained thin sections of the aggregates revealed the absence of any necrosis. Confocal microscopy evaluations of cells stained with the Live/Dead assay (Molecular Probes) confirmed that viable cells were present throughout the aggregates with an average of only three dead cells observed per aggregate. Preliminary results from gene array analysis (Affymetrix chip U74Av2) showed that approximately 14% of the genes were down regulated (decreased more than 3 fold) and 4% were upregulated in cells exposed to modeled microgravity for 12 hours compared to unit gravity controls. Additional studies using fluorescent phallacidin revealed a decrease in F-actin in the cells exposed to modeled microgravity compared to unit gravity. Myoblast cells grown as aggregates in modeled microgravity exhibited spontaneous differentiation into syncitia while no differentiation was seen in the unit gravity controls. These studies show that 1)the model test system developed is suitable for assessing cellular and molecular alterations in myoblasts; 2) gene expression alterations occur rapidly (within 12 hours) following exposure to modeled microgravity; and 3) modeled microgravity conditions stimulated myoblast cell differentiation. Achieving a greater understanding of the molecular alterations leading to muscle atrophy will eventually enable the development of cell-based countermeasures, which may be valuable for treatment of muscle diseases on

  16. Model multilayer structures for three-dimensional cell imaging

    NASA Astrophysics Data System (ADS)

    Kozole, Joseph; Szakal, Christopher; Kurczy, Michael; Winograd, Nicholas

    2006-07-01

    The prospects for SIMS three-dimensional analysis of biological materials were explored using model multilayer structures. The samples were analyzed in a ToF-SIMS spectrometer equipped with a 20 keV buckminsterfullerene (C 60+) ion source. Molecular depth information was acquired using a C 60+ ion beam to etch through the multilayer structures at specified time intervals. Subsequent to each individual erosion cycle, static SIMS spectra were recorded using a pulsed C 60+ ion probe. Molecular intensities in sequential mass spectra were monitored as a function of primary ion fluence. The resulting depth information was used to characterize C 60+ bombardment of biological materials. Specifically, molecular depth profile studies involving dehydrated dipalmitoyl-phosphatidylcholine (DPPC) organic films indicate that cell membrane lipid materials do not experience significant chemical damage when bombarded with C 60+ ion fluences greater than 10 15 ions/cm 2. Moreover, depth profile analyses of DPPC-sucrose frozen multilayer structures suggest that biomolecule information can be uncovered after the C 60+ sputter removal of a 20 nm overlayer with no appreciable loss of underlying molecular signal. The experimental results support the potential for three-dimensional molecular mapping of biological materials using cluster SIMS.

  17. A Three-Dimensional Parallel Time-Accurate Turbopump Simulation Procedure Using Overset Grid System

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Chan, William; Kwak, Dochan

    2002-01-01

    The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and nonuniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete simulation of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate simulations with moving boundary capability are presented along with the performance of parallel versions of the code.

  18. A Three Dimensional Parallel Time Accurate Turbopump Simulation Procedure Using Overset Grid Systems

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Chan, William; Kwak, Dochan

    2001-01-01

    The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort provides developers with information such as transient flow phenomena at start up, and non-uniform inflows, and will eventually impact on system vibration and structures. In the proposed paper, the progress toward the capability of complete simulation of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. CAD to solution auto-scripting capability is being developed for turbopump applications. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 3000 systems at NASA Ames Research Center. Results from these time-accurate simulations with moving boundary capability will be presented along with the performance of parallel versions of the code.

  19. MODELING THREE-DIMENSIONAL MORPHOLOGICAL STRUCTURES USING SPHERICAL HARMONICS

    PubMed Central

    Shen, Li; Farid, Hany; McPeek, Mark A.

    2010-01-01

    Quantifying morphological shape is a fundamental issue in evolutionary biology. Recent technological advances (e.g., confocal microscopy, laser scanning, computer tomography) have made the capture of detailed three-dimensional (3D) morphological structure easy and cost-effective. In this article, we develop a 3D analytic framework (SPHARM—spherical harmonics) for modeling the shapes of complex morphological structures from continuous surface maps that can be produced by these technologies. Because the traditional SPHARM methodology has limitations in several of its processing steps, we present new algorithms for two SPHARM processing steps: spherical parameterization and SPHARM registration. These new algorithms allow for the numerical characterization of a much larger class of 3D models. We demonstrate the effectiveness of the method by applying it to modeling the cerci of Enallagma damselflies. PMID:19154365

  20. Three-dimensional temporomandibular joint modeling and animation.

    PubMed

    Cascone, Piero; Rinaldi, Fabrizio; Pagnoni, Mario; Marianetti, Tito Matteo; Tedaldi, Massimiliano

    2008-11-01

    The three-dimensional (3D) temporomandibular joint (TMJ) model derives from a study of the cranium by 3D virtual reality and mandibular function animation. The starting point of the project is high-fidelity digital acquisition of a human dry skull. The cooperation between the maxillofacial surgeon and the cartoonist enables the reconstruction of the fibroconnective components of the TMJ that are the keystone for comprehension of the anatomic and functional features of the mandible. The skeletal model is customized with the apposition of the temporomandibular ligament, the articular disk, the retrodiskal tissue, and the medial and the lateral ligament of the disk. The simulation of TMJ movement is the result of the integration of up-to-date data on the biomechanical restrictions. The 3D TMJ model is an easy-to-use application that may be run on a personal computer for the study of the TMJ and its biomechanics. PMID:19098544

  1. Three-Dimensional Numerical Modeling of Magnetohydrodynamic Augmented Propulsion Experiment

    NASA Technical Reports Server (NTRS)

    Turner, M. W.; Hawk, C. W.; Litchford, R. J.

    2009-01-01

    Over the past several years, NASA Marshall Space Flight Center has engaged in the design and development of an experimental research facility to investigate the use of diagonalized crossed-field magnetohydrodynamic (MHD) accelerators as a possible thrust augmentation device for thermal propulsion systems. In support of this effort, a three-dimensional numerical MHD model has been developed for the purpose of analyzing and optimizing accelerator performance and to aid in understanding critical underlying physical processes and nonideal effects. This Technical Memorandum fully summarizes model development efforts and presents the results of pretest performance optimization analyses. These results indicate that the MHD accelerator should utilize a 45deg diagonalization angle with the applied current evenly distributed over the first five inlet electrode pairs. When powered at 100 A, this configuration is expected to yield a 50% global efficiency with an 80% increase in axial velocity and a 50% increase in centerline total pressure.

  2. TRANSMISSION SPECTRA OF THREE-DIMENSIONAL HOT JUPITER MODEL ATMOSPHERES

    SciTech Connect

    Fortney, J. J.; Shabram, M.; Showman, A. P.; Lian, Y.; Lewis, N. K.; Freedman, R. S.; Marley, M. S.

    2010-02-01

    We compute models of the transmission spectra of planets HD 209458b, HD 189733b, and generic hot Jupiters. We examine the effects of temperature, surface gravity, and metallicity for the generic planets as a guide to understanding transmission spectra in general. We find that carbon dioxide absorption at 4.4 and 15 mum is prominent at high metallicity, and is a clear metallicity indicator. For HD 209458b and HD 189733b, we compute spectra for both one-dimensional and three-dimensional model atmospheres and examine the differences between them. The differences are usually small, but can be large if atmospheric temperatures are near important chemical abundance boundaries. The calculations for the three-dimensional atmospheres, and their comparison with data, serve as constraints on these dynamical models that complement the secondary eclipse and light curve data sets. For HD 209458b, even if TiO and VO gases are abundant on the dayside, their abundances can be considerably reduced on the cooler planetary limb. However, given the predicted limb temperatures and TiO abundances, the model's optical opacity is too high. For HD 189733b we find a good match with some infrared data sets and constrain the altitude of a postulated haze layer. For this planet, substantial differences can exist between the transmission spectra of the leading and trailing hemispheres, which are an excellent probe of carbon chemistry. In thermochemical equilibrium, the cooler leading hemisphere is methane-dominated, and the hotter trailing hemisphere is CO-dominated, but these differences may be eliminated by non-equilibrium chemistry due to vertical mixing. It may be possible to constrain the carbon chemistry of this planet, and its spatial variation, with James Webb Space Telescope.

  3. Three-dimensional lattice Boltzmann model for compressible flows.

    PubMed

    Sun, Chenghai; Hsu, Andrew T

    2003-07-01

    A three-dimensional compressible lattice Boltzmann model is formulated on a cubic lattice. A very large particle-velocity set is incorporated in order to enable a greater variation in the mean velocity. Meanwhile, the support set of the equilibrium distribution has only six directions. Therefore, this model can efficiently handle flows over a wide range of Mach numbers and capture shock waves. Due to the simple form of the equilibrium distribution, the fourth-order velocity tensors are not involved in the formulation. Unlike the standard lattice Boltzmann model, no special treatment is required for the homogeneity of fourth-order velocity tensors on square lattices. The Navier-Stokes equations were recovered, using the Chapman-Enskog method from the Bhatnagar-Gross-Krook (BGK) lattice Boltzmann equation. The second-order discretization error of the fluctuation velocity in the macroscopic conservation equation was eliminated by means of a modified collision invariant. The model is suitable for both viscous and inviscid compressible flows with or without shocks. Since the present scheme deals only with the equilibrium distribution that depends only on fluid density, velocity, and internal energy, boundary conditions on curved wall are easily implemented by an extrapolation of macroscopic variables. To verify the scheme for inviscid flows, we have successfully simulated a three-dimensional shock-wave propagation in a box and a normal shock of Mach number 10 over a wedge. As an application to viscous flows, we have simulated a flat plate boundary layer flow, flow over a cylinder, and a transonic flow over a NACA0012 airfoil cascade.

  4. Three dimensional CAD model of the Ignitor machine

    NASA Astrophysics Data System (ADS)

    Orlandi, S.; Zanaboni, P.; Macco, A.; Sioli, V.; Risso, E.

    1998-11-01

    defind The final, global product of all the structural and thermomechanical design activities is a complete three dimensional CAD (AutoCAD and Intergraph Design Review) model of the IGNITOR machine. With this powerful tool, any interface, modification, or upgrading of the machine design is managed as an integrated part of the general effort aimed at the construction of the Ignitor facility. ind The activities that are underway, to complete the design of the core of the experiment and that will be described, concern the following: ind - the cryogenic cooling system, ind - the radial press, the center post, the mechanical supports (legs) of the entire machine, ind - the inner mechanical supports of major components such as the plasma chamber and the outer poloidal field coils.

  5. Three-dimensional antenna models for fusion experiments

    NASA Astrophysics Data System (ADS)

    Carter, M. D.; Wang, C. Y.; Hogan, J. T.; Harris, J. H.; Hoffman, D. J.; Rasmussen, D. A.; Ryan, P. M.; Stallings, D. S.; Batchelor, D. B.; Beaumont, B.; Hutter, T.; Saoutic, B.

    1996-02-01

    The development of the RANT3D code has permitted the systematic study of the effect of three-dimensional structures on the launched power spectrum for antennas in the ion cyclotron range of frequencies. The code allows the septa between current straps to be modeled with arbitrary heights and permits the antenna to interact with other structures in the tokamak. In this paper we present comparisons of calculated loading with the Tokamak Fusion Test Reactor and Tore Supra experiments, demonstrate the effects on loading caused by positioning uncertainties for an antenna in Tore Supra, and show electric field patterns near the Tore Supra antenna. A poloidal component in the static magnetic field for the plasma response is included in the near-field calculations using the warm plasma code, GLOSI. Preliminary estimates for the heat flux on the bumper limiters during typical operation in Tore Supra are also presented.

  6. Generation of animation sequences of three dimensional models

    NASA Technical Reports Server (NTRS)

    Poi, Sharon (Inventor); Bell, Brad N. (Inventor)

    1990-01-01

    The invention is directed toward a method and apparatus for generating an animated sequence through the movement of three-dimensional graphical models. A plurality of pre-defined graphical models are stored and manipulated in response to interactive commands or by means of a pre-defined command file. The models may be combined as part of a hierarchical structure to represent physical systems without need to create a separate model which represents the combined system. System motion is simulated through the introduction of translation, rotation and scaling parameters upon a model within the system. The motion is then transmitted down through the system hierarchy of models in accordance with hierarchical definitions and joint movement limitations. The present invention also calls for a method of editing hierarchical structure in response to interactive commands or a command file such that a model may be included, deleted, copied or moved within multiple system model hierarchies. The present invention also calls for the definition of multiple viewpoints or cameras which may exist as part of a system hierarchy or as an independent camera. The simulated movement of the models and systems is graphically displayed on a monitor and a frame is recorded by means of a video controller. Multiple movement and hierarchy manipulations are then recorded as a sequence of frames which may be played back as an animation sequence on a video cassette recorder.

  7. A THREE-DIMENSIONAL BABCOCK-LEIGHTON SOLAR DYNAMO MODEL

    SciTech Connect

    Miesch, Mark S.; Dikpati, Mausumi

    2014-04-10

    We present a three-dimensional (3D) kinematic solar dynamo model in which poloidal field is generated by the emergence and dispersal of tilted sunspot pairs (more generally bipolar magnetic regions, or BMRs). The axisymmetric component of this model functions similarly to previous 2.5 dimensional (2.5D, axisymmetric) Babcock-Leighton (BL) dynamo models that employ a double-ring prescription for poloidal field generation but we generalize this prescription into a 3D flux emergence algorithm that places BMRs on the surface in response to the dynamo-generated toroidal field. In this way, the model can be regarded as a unification of BL dynamo models (2.5D in radius/latitude) and surface flux transport models (2.5D in latitude/longitude) into a more self-consistent framework that builds on the successes of each while capturing the full 3D structure of the evolving magnetic field. The model reproduces some basic features of the solar cycle including an 11 yr periodicity, equatorward migration of toroidal flux in the deep convection zone, and poleward propagation of poloidal flux at the surface. The poleward-propagating surface flux originates as trailing flux in BMRs, migrates poleward in multiple non-axisymmetric streams (made axisymmetric by differential rotation and turbulent diffusion), and eventually reverses the polar field, thus sustaining the dynamo. In this Letter we briefly describe the model, initial results, and future plans.

  8. Three-dimensional cardiac computational modelling: methods, features and applications.

    PubMed

    Lopez-Perez, Alejandro; Sebastian, Rafael; Ferrero, Jose M

    2015-01-01

    The combination of computational models and biophysical simulations can help to interpret an array of experimental data and contribute to the understanding, diagnosis and treatment of complex diseases such as cardiac arrhythmias. For this reason, three-dimensional (3D) cardiac computational modelling is currently a rising field of research. The advance of medical imaging technology over the last decades has allowed the evolution from generic to patient-specific 3D cardiac models that faithfully represent the anatomy and different cardiac features of a given alive subject. Here we analyse sixty representative 3D cardiac computational models developed and published during the last fifty years, describing their information sources, features, development methods and online availability. This paper also reviews the necessary components to build a 3D computational model of the heart aimed at biophysical simulation, paying especial attention to cardiac electrophysiology (EP), and the existing approaches to incorporate those components. We assess the challenges associated to the different steps of the building process, from the processing of raw clinical or biological data to the final application, including image segmentation, inclusion of substructures and meshing among others. We briefly outline the personalisation approaches that are currently available in 3D cardiac computational modelling. Finally, we present examples of several specific applications, mainly related to cardiac EP simulation and model-based image analysis, showing the potential usefulness of 3D cardiac computational modelling into clinical environments as a tool to aid in the prevention, diagnosis and treatment of cardiac diseases. PMID:25928297

  9. Three-dimensional effects for radio frequency antenna modeling

    NASA Astrophysics Data System (ADS)

    Carter, M. D.; Batchelor, D. B.; Stallings, D. C.

    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 by 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.

  10. Three-dimensional effects for radio frequency antenna modeling

    NASA Astrophysics Data System (ADS)

    Carter, M. D.; Batchelor, D. B.; Stallings, D. C.

    1994-10-01

    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 by 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.

  11. Three-dimensional Model of Tissue and Heavy Ions Effects

    NASA Technical Reports Server (NTRS)

    Ponomarev, Artem L.; Sundaresan, Alamelu; Huff, Janice L.; Cucinotta, Francis A.

    2007-01-01

    A three-dimensional tissue model was incorporated into a new Monte Carlo algorithm that simulates passage of heavy ions in a tissue box . The tissue box was given as a realistic model of tissue based on confocal microscopy images. The action of heavy ions on the cellular matrix for 2- or 3-dimensional cases was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix), and as a multi-layer obtained from confocal microscopy (3-d case). Image segmentation was used to identify cells with precise areas/volumes in an irradiated cell culture monolayer, and slices of tissue with many cell layers. The cells were then inserted into the model box of the simulated physical space pixel by pixel. In the case of modeled tissues (3-d), the tissue box had periodic boundary conditions imposed, which extrapolates the technique to macroscopic volumes of tissue. For the real tissue (3-d), specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated from current experimental data. A spatial correlation function indicating a higher spatial concentration of damaged cells from heavy ions relative to the low-LET radiation cell damage pattern is presented. The spatial correlation effects among necrotic cells can help studying microlesions in organs, and probable effects of directionality of heavy ion radiation on epithelium and endothelium.

  12. Three dimensional water quality modeling of a shallow subtropical estuary.

    PubMed

    Wan, Yongshan; Ji, Zhen-Gang; Shen, Jian; Hu, Guangdou; Sun, Detong

    2012-12-01

    Knowledge of estuarine hydrodynamics and water quality comes mostly from studies of large estuarine systems. The processes affecting algae, nutrients, and dissolved oxygen (DO) in small and shallow subtropical estuaries are relatively less studied. This paper documents the development, calibration, and verification of a three dimensional (3D) water quality model for the St. Lucie Estuary (SLE), a small and shallow estuary located on the east coast of south Florida. The water quality model is calibrated and verified using two years of measured data. Statistical analyses indicate that the model is capable of reproducing key water quality characteristics of the estuary within an acceptable range of accuracy. The calibrated model is further applied to study hydrodynamic and eutrophication processes in the estuary. Modeling results reveal that high algae concentrations in the estuary are likely caused by excessive nutrient and algae supplies in freshwater inflows. While algal blooms may lead to reduced DO concentrations near the bottom of the waterbody, this study indicates that stratification and circulation induced by freshwater inflows may also contribute significantly to bottom water hypoxia in the estuary. It is also found that high freshwater inflows from one of the tributaries can change the circulation pattern and nutrient loading, thereby impacting water quality conditions of the entire estuary. Restoration plans for the SLE ecosystem need to consider both a reduction of nutrient loading and regulation of the freshwater discharge pattern.

  13. Three-dimensional lattice Boltzmann model for magnetic reconnection

    SciTech Connect

    Mendoza, M.; Munoz, J. D.

    2008-02-15

    We develop a three-dimensional (3D) lattice Boltzmann model that recovers in the continuous limit the two-fluids theory for plasmas, and consequently includes the generalized Ohm's law. The model reproduces the magnetic reconnection process just by giving the right initial equilibrium conditions in the magnetotail, without any assumption on the resistivity in the diffusive region. In this model, the plasma is handled similar to two fluids with an interaction term, each one with distribution functions associated to a cubic lattice with 19 velocities (D3Q19). The electromagnetic fields are considered as a third fluid with an external force on a cubic lattice with 13 velocities (D3Q13). The model can simulate either viscous fluids in the incompressible limit or nonviscous compressible fluids, and successfully reproduces both the Hartmann flow and the magnetic reconnection in the magnetotail. The reconnection rate in the magnetotail obtained with this model lies between R=0.062 and R=0.073, in good agreement with the observations.

  14. Three-dimensional lattice Boltzmann model for magnetic reconnection.

    PubMed

    Mendoza, M; Muñoz, J D

    2008-02-01

    We develop a three-dimensional (3D) lattice Boltzmann model that recovers in the continuous limit the two-fluids theory for plasmas, and consequently includes the generalized Ohm's law. The model reproduces the magnetic reconnection process just by giving the right initial equilibrium conditions in the magnetotail, without any assumption on the resistivity in the diffusive region. In this model, the plasma is handled similar to two fluids with an interaction term, each one with distribution functions associated to a cubic lattice with 19 velocities (D3Q19). The electromagnetic fields are considered as a third fluid with an external force on a cubic lattice with 13 velocities (D3Q13). The model can simulate either viscous fluids in the incompressible limit or nonviscous compressible fluids, and successfully reproduces both the Hartmann flow and the magnetic reconnection in the magnetotail. The reconnection rate in the magnetotail obtained with this model lies between R=0.062 and R=0.073, in good agreement with the observations.

  15. A three-dimensional model of Tangential YORP

    SciTech Connect

    Golubov, O.; Scheeres, D. J.; Krugly, Yu. N.

    2014-10-10

    Tangential YORP, or TYORP, has recently been demonstrated to be an important factor in the evolution of an asteroid's rotation state. It is complementary to normal YORP, or NYORP, which used to be considered previously. While NYORP is produced by non-symmetry in the large-scale geometry of an asteroid, TYORP is due to heat conductivity in stones on the surface of the asteroid. To date, TYORP has been studied only in a simplified one-dimensional model, substituting stones with high long walls. This article for the first time considers TYORP in a realistic three-dimensional model, also including shadowing and self-illumination effects via ray tracing. TYORP is simulated for spherical stones lying on regolith. The model includes only five free parameters and the dependence of the TYORP on each of them is studied. The TYORP torque appears to be smaller than previous estimates from the one-dimensional model, but is still comparable to the NYORP torques. These results can be used to estimate TYORP of different asteroids and also as a basis for more sophisticated models of TYORP.

  16. A Three-Dimensional Computational Model of Collagen Network Mechanics

    PubMed Central

    Lee, Byoungkoo; Zhou, Xin; Riching, Kristin; Eliceiri, Kevin W.; Keely, Patricia J.; Guelcher, Scott A.; Weaver, Alissa M.; Jiang, Yi

    2014-01-01

    Extracellular matrix (ECM) strongly influences cellular behaviors, including cell proliferation, adhesion, and particularly migration. In cancer, the rigidity of the stromal collagen environment is thought to control tumor aggressiveness, and collagen alignment has been linked to tumor cell invasion. While the mechanical properties of collagen at both the single fiber scale and the bulk gel scale are quite well studied, how the fiber network responds to local stress or deformation, both structurally and mechanically, is poorly understood. This intermediate scale knowledge is important to understanding cell-ECM interactions and is the focus of this study. We have developed a three-dimensional elastic collagen fiber network model (bead-and-spring model) and studied fiber network behaviors for various biophysical conditions: collagen density, crosslinker strength, crosslinker density, and fiber orientation (random vs. prealigned). We found the best-fit crosslinker parameter values using shear simulation tests in a small strain region. Using this calibrated collagen model, we simulated both shear and tensile tests in a large linear strain region for different network geometry conditions. The results suggest that network geometry is a key determinant of the mechanical properties of the fiber network. We further demonstrated how the fiber network structure and mechanics evolves with a local formation, mimicking the effect of pulling by a pseudopod during cell migration. Our computational fiber network model is a step toward a full biomechanical model of cellular behaviors in various ECM conditions. PMID:25386649

  17. A three-dimensional transport model for the middle atmosphere

    NASA Technical Reports Server (NTRS)

    Rasch, Philip J.; Tie, Xuexi; Boville, Byron A.; Williamson, David L.

    1994-01-01

    In this paper we describe fundamental properties of an 'off-line' three-dimensional transport model, that is, a model which uses prescribed rather than predicted winds. The model is currently used primarily for studying problems of the middle atmosphere because we have not (yet) incorporated a formulation for the convective transport of trace species, a prerequisite for many tropospheric problems. The off-line model is simpler and less expensive than a model which predicts the wind and mass evolution (an 'on-line' model), but it is more complex than the two-dimensional (2-D) zonally averaged transport models often used in the study of chemistry and transport in the middle atmosphere. It thus serves as a model of intermediate complexity and can fill a useful niche for the study of transport and chemistry. We compare simulations of four tracers, released in the lower stratosphere, in both the on- and off-line models to document the difference resulting from differences in modeling the same problem with this intermediate model. These differences identify the price to be paid in going to a cheaper and simpler calculation. The off-line model transports a tracer in three dimensions. For this reason, it requires fewer approximations than 2-D transport model, which must parameterize the effects of mixing by transient and zonally asymmetric wind features. We compare simulations of the off-line model with simulations of a 2-D model for two problems. First, we compare 2-D and three-dimensional (3-D) models by simulating the emission of an NO(x)-like tracer by a fleet of high-speed aircraft. The off-line model is then used to simulate the transport of C-14 and to contrast its simulation properties to that of the host of 2-D models which participated in an identical simulation in a recent NASA model intercomparison. The off-line model is shown to be somewhat sensitive to the sampling strategy for off-line winds. Simulations with daily averaged winds are in very good qualitative

  18. Development of an interactive anatomical three-dimensional eye model.

    PubMed

    Allen, Lauren K; Bhattacharyya, Siddhartha; Wilson, Timothy D

    2015-01-01

    The discrete anatomy of the eye's intricate oculomotor system is conceptually difficult for novice students to grasp. This is problematic given that this group of muscles represents one of the most common sites of clinical intervention in the treatment of ocular motility disorders and other eye disorders. This project was designed to develop a digital, interactive, three-dimensional (3D) model of the muscles and cranial nerves of the oculomotor system. Development of the 3D model utilized data from the Visible Human Project (VHP) dataset that was refined using multiple forms of 3D software. The model was then paired with a virtual user interface in order to create a novel 3D learning tool for the human oculomotor system. Development of the virtual eye model was done while attempting to adhere to the principles of cognitive load theory (CLT) and the reduction of extraneous load in particular. The detailed approach, digital tools employed, and the CLT guidelines are described herein. PMID:25228501

  19. Three-dimensional antiferromagnetic CP(N-1) models.

    PubMed

    Delfino, Francesco; Pelissetto, Andrea; Vicari, Ettore

    2015-05-01

    We investigate the critical behavior of three-dimensional antiferromagnetic CP(N-1) (ACP(N-1)) models in cubic lattices, which are characterized by a global U(N) symmetry and a local U(1) gauge symmetry. Assuming that critical fluctuations are associated with a staggered gauge-invariant (Hermitian traceless matrix) order parameter, we determine the corresponding Landau-Ginzburg-Wilson (LGW) model. For N=3 this mapping allows us to conclude that the three-component ACP(2) model undergoes a continuous transition that belongs to the O(8) vector universality class, with an effective enlargement of the symmetry at the critical point. This prediction is confirmed by numerical analyses of the finite-size scaling behaviors of the ACP(2) and the O(8) vector models, which show the same universal features at their transitions. We also present a renormalization-group (RG) analysis of the LGW theories for N≥4. We compute perturbative series in two different renormalization schemes and analyze the corresponding RG flow. We do not find stable fixed points that can be associated with continuous transitions. PMID:26066121

  20. Three-dimensional lattice Boltzmann model for electrodynamics.

    PubMed

    Mendoza, M; Muñoz, J D

    2010-11-01

    In this paper we introduce a three-dimensional Lattice-Boltzmann model that recovers in the continuous limit the Maxwell equations in materials. In order to build conservation equations with antisymmetric tensors, like the Faraday law, the model assigns four auxiliary vectors to each velocity vector. These auxiliary vectors, when combined with the distribution functions, give the electromagnetic fields. The evolution is driven by the usual Bhatnager-Gross-Krook (BGK) collision rule, but with a different form for the equilibrium distribution functions. This lattice Bhatnager-Gross-Krook (LBGK) model allows us to consider for both dielectrics and conductors with realistic parameters, and therefore it is adequate to simulate the most diverse electromagnetic problems, like the propagation of electromagnetic waves (both in dielectric media and in waveguides), the skin effect, the radiation pattern of a small dipole antenna and the natural frequencies of a resonant cavity, all with 2% accuracy. Actually, it shows to be one order of magnitude faster than the original Finite-difference time-domain (FDTD) formulation by Yee to reach the same accuracy. It is, therefore, a valuable alternative to simulate electromagnetic fields and opens lattice Boltzmann for a broad spectrum of new applications in electrodynamics.

  1. Three-dimensional model of cytochrome P450 human aromatase.

    PubMed

    Loge, Cedric; Le Borgne, Marc; Marchand, Pascal; Robert, Jean-Michel; Le Baut, Guillaume; Palzer, Martina; Hartmann, Rolf W

    2005-12-01

    A three-dimensional (3-D) structure of human aromatase (CYP 19) was modeled on the basis of the crystal structure of rabbit CYP2C5, the first solved X-ray structure of an eukaryotic cytochrome P450 and was evaluated by docking S-fadrozole and the steroidal competitive inhibitor (19R)-10-thiiranylestr-4-ene-3,17-dione, into the enzyme active site. According to a previous pharmacophoric hypothesis described in the literature, the cyano group of S-fadrozole partially mimics the steroid backbone C(17) carbonyl group of (19R)-10-thiiranylestr-4-ene-3,17-dione, and was oriented in a favorable position for H-bonding with the newly identified positively charged residues Lys 119 and Arg435. In addition, this model is consistent with the recent combined mutagenesis/modeling studies already published concerning the roles ofAsp309 and His480 in the aromatization of the steroid A ring. PMID:16408794

  2. Three-dimensional bonded-cell model for grain fragmentation

    NASA Astrophysics Data System (ADS)

    Cantor, D.; Azéma, E.; Sornay, P.; Radjai, F.

    2016-07-01

    We present a three-dimensional numerical method for the simulation of particle crushing in 3D. This model is capable of producing irregular angular fragments upon particle fragmentation while conserving the total volume. The particle is modeled as a cluster of rigid polyhedral cells generated by a Voronoi tessellation. The cells are bonded along their faces by a cohesive Tresca law with independent tensile and shear strengths and simulated by the contact dynamics method. Using this model, we analyze the mechanical response of a single particle subjected to diametral compression for varying number of cells, their degree of disorder, and intercell tensile and shear strength. In particular, we identify the functional dependence of particle strength on the intercell strengths. We find that two different regimes can be distinguished depending on whether intercell shear strength is below or above its tensile strength. In both regimes, we observe a power-law dependence of particle strength on both intercell strengths but with different exponents. The strong effect of intercell shear strength on the particle strength reflects an interlocking effect between cells. In fact, even at low tensile strength, the particle global strength can still considerably increase with intercell shear strength. We finally show that the Weibull statistics describes well the particle strength variability.

  3. Three-dimensional computer modeling of hydrogen injection and combustion

    SciTech Connect

    Johnson, N.L.; Amsden, A.A.; Naber, J.D.; Siebers, D.L.

    1995-02-01

    The hydrodynamics of hydrogen gas injection into a fixed-volume combustion chamber is analyzed and simulated using KIVA-3, a three-dimensional, reactive flow computer code. Comparisons of the simulation results are made to data obtained at the Combustion Research Facility at Sandia National Laboratory-California (SNL-CA). Simulation of the gas injection problem is found to be of comparable difficulty as the liquid fuel injection in diesel engines. The primary challenge is the large change of length scale from the flow of gas in the orifice to the penetration in the combustion chamber. In the current experiments, the change of length scale is about 4,000. A reduction of the full problem is developed that reduces the change in length scale in the simulation to about 400, with a comparable improvement in computational times. Comparisons of the simulation to the experimental data shows good agreement in the penetration history and pressure rise in the combustion chamber. At late times the comparison is sensitive to the method of determination of the penetration in the simulations. In a comparison of the combustion modeling of methane and hydrogen, hydrogen combustion is more difficult to model, and currently available kinetic models fail to predict the observed autoignition delay at these conditions.

  4. THREE-DIMENSIONAL MODELING OF HOT JUPITER ATMOSPHERIC FLOWS

    SciTech Connect

    Rauscher, Emily; Menou, Kristen

    2010-05-10

    We present a three-dimensional hot Jupiter model, extending from 200 bar to 1 mbar, using the Intermediate General Circulation Model from the University of Reading. Our horizontal spectral resolution is T31 (equivalent to a grid of 48 x 96), with 33 logarithmically spaced vertical levels. A simplified (Newtonian) scheme is employed for the radiative forcing. We adopt a physical setup nearly identical to the model of HD 209458b by Cooper and Showman to facilitate a direct model inter-comparison. Our results are broadly consistent with theirs but significant differences also emerge. The atmospheric flow is characterized by a super-rotating equatorial jet, transonic wind speeds, and eastward advection of heat away from the dayside. We identify a dynamically induced temperature inversion ('stratosphere') on the planetary dayside and find that temperatures at the planetary limb differ systematically from local radiative equilibrium values, a potential source of bias for transit spectroscopic interpretations. While our model atmosphere is quasi-identical to that of Cooper and Showman and we solve the same meteorological equations, we use different algorithmic methods, spectral-implicit versus grid-explicit, which are known to yield fully consistent results in the Earth modeling context. The model discrepancies identified here indicate that one or both numerical methods do not faithfully capture all of the atmospheric dynamics at work in the hot Jupiter context. We highlight the emergence of a shock-like feature in our model, much like that reported recently by Showman et al., and suggest that improved representations of energy conservation may be needed in hot Jupiter atmospheric models, as emphasized by Goodman.

  5. Three Dimensional TEM Forward Modeling Using FDTD Accelerated by GPU

    NASA Astrophysics Data System (ADS)

    Li, Z.; Huang, Q.

    2015-12-01

    Three dimensional inversion of transient electromagnetic (TEM) data is still challenging. The inversion speed mostly depends on the forward modeling. Finite-difference time-domain (FDTD) method is one of the popular forward modeling scheme. In an explicit type, which is based on the Du Fort-Frankel scheme, the time step is under the constraint of quasi-static approximation. Often an upward-continuation boundary condition (UCBC) is applied on the earth-air surface to avoid time stepping in the model air. However, UCBC is not suitable for models with topography and has a low parallel efficiency. Modeling without UCBC may cause a much smaller time step because of the resistive attribute of the air and the quasi-static constraint, which may also low the efficiency greatly. Our recent research shows that the time step in the model air is not needed to be constrained by the quasi-static approximation, which can let the time step without UCBC much closer to that with UCBC. The parallel performance of FDTD is then largely released. On a computer with a 4-core CPU, this newly developed method is obviously faster than the method using UCBC. Besides, without UCBC, this method can be easily accelerated by Graphics Processing Unit (GPU). On a computer with a CPU of 4790k@4.4GHz and a GPU of GTX 970, the speed accelerated by CUDA is almost 10 times of that using CPU only. For a model with a grid size of 140×140×130, if the conductivity of the model earth is 0.02S/m, and the minimal space interval is 15m, it takes only 80 seconds to evolve the field from excitation to 0.032s.

  6. Three-Dimensional Modeling of Quasi-Homologous Solar Jets

    NASA Technical Reports Server (NTRS)

    Pariat, E.; Antiochos, S. K.; DeVore, C. R.

    2010-01-01

    Recent solar observations (e.g., obtained with Hinode and STEREO) have revealed that coronal jets are a more frequent phenomenon than previously believed. This higher frequency results, in part, from the fact that jets exhibit a homologous behavior: successive jets recur at the same location with similar morphological features. We present the results of three-dimensional (31)) numerical simulations of our model for coronal jets. This study demonstrates the ability of the model to generate recurrent 3D untwisting quasi-homologous jets when a stress is constantly applied at the photospheric boundary. The homology results from the property of the 3D null-point system to relax to a state topologically similar to its initial configuration. In addition, we find two distinct regimes of reconnection in the simulations: an impulsive 3D mode involving a helical rotating current sheet that generates the jet, and a quasi-steady mode that occurs in a 2D-like current sheet located along the fan between the sheared spines. We argue that these different regimes can explain the observed link between jets and plumes.

  7. Modelling for three dimensional coalescence of two bubbles

    NASA Astrophysics Data System (ADS)

    Han, R.; Li, S.; Zhang, A. M.; Wang, Q. X.

    2016-06-01

    This paper is concerned with the three dimensional (3D) interaction and coalescence of two bubbles subject to buoyancy and the dynamics of the subsequent joined bubble using the boundary integral method (BIM). An improved density potential method is implemented to control the mesh quality. It helps to avoid the numerical instabilities, which occur after coalescence. Numerical convergence tests are conducted in terms of mesh sizes and time steps. The 3D numerical model agrees well with an axisymmetric BIM model for axisymmetric cases as well as experimental results captured by high-speed camera. The bubble jetting, interaction, and coalescence of the two bubbles depend on the maximum bubble radii, the centre distance between two bubbles at inception, and the angle β between the centre line and the direction of buoyancy. We investigate coalescence of two bubbles for β = 0, π/4, and π/2, respectively, and at various centre distances at inception. Numerical results presented include the bubble and jet shapes, the velocity, and pressure fields surrounding the bubbles, as well as the time histories of bubble volumes, jet velocities, and positions of centroid of the bubble system.

  8. Three-dimensional high-resolution plasma bubble modeling

    NASA Astrophysics Data System (ADS)

    Yokoyama, Tatsuhiro; Shinagawa, Hiroyuki; Jin, Hidekatsu

    Equatorial plasma bubble (EPB) is a well-known phenomenon in the equatorial ionospheric F region. As it causes severe scintillation in the amplitude and phase of radio signals, it is important to understand and forecast the occurrence of EPB from a space weather point of view. The development of EPB is known as a evolution of the generalized Rayleigh-Taylor instability. Numerical modelings of the instability on the equatorial two-dimensional plane have been conducted since the late 1970's, and the nonlinear evolution of the instability has been clearly presented. Recently, three-dimensional (3D) modelings became popular tools for further understanding of the development of EPB such as 3D structure of EPB, meridional wind effects and gravity wave seeding. One of the biggest advantages of the 3D model is that the off-equatorial E region which is coupled with the equatorial F region can be included in the model. It is known from observations that the conductance of the off-equatorial E region controls the growth rate of the Rayleigh-Taylor instability, that is, sudden decrease of the E-region conductance around the sunset accelerates the evolution of the instability. We have developed a new 3D high-resolution model for EPB, and studied internal structure of EPB and the contribution of the off-equatorial E region. As it is necessary to use high-order numerical schemes to capture sharp plasma density gradient of EPB, we adopted the CIP scheme which can keep the third-order accuracy in time and space. The simulated EPB has asymmetrical density gradients at east and west walls, and the growth rate changes significantly depending on the condition of the off-equatorial E region. In the future, we will integrate the high-resolution model into whole atmosphere-ionosphere coupled model (GAIA) to study the growth of EPB under the realistic background conditions.

  9. Three-dimensional modeling of plastic deformation flow during ECAP

    SciTech Connect

    Budilov, I. N.; Alexandrov, I. V.; Beyerlein, Irene J.; Lukaschuk, Y. V.; Zhernakov, V. S.

    2004-01-01

    ECAP. In this work, we present preliminary results using a three dimensional (3D) FE code for simulating ECAP. The influence of the outer die radius and friction coefficient on the accumulated plastic strain in a single ECAP pass of pure Cu (99.9%) is investigated. Special attention is paid to the heterogeneity in strain along the billet length, from top to bottom, and side to side. We will also compare the simulated punch force vs displacement curve with the experimental curve to access the accuracy of the material and friction models.

  10. Three dimensional numerical modeling of land subsidence in Shanghai

    NASA Astrophysics Data System (ADS)

    Ye, S.; Luo, Y.; Wu, J.; Teatini, P.; Wang, H.; Jiao, X.

    2015-11-01

    Shanghai city has been suffering land subsidence caused by overly exploitation of ground water since 1921, which is a serious problem for this coastal city with altitude of 2.2-4.8 m above mean sea level. The largest cumulative land subsidence amounted to 2.6 m in the downtown area. Measures to decrease the ground water exploitation, change the pumping aquifers, and increase aquifer artificial recharge have been used to mitigate land subsidence since 1961. It is necessary to develop a proper numerical model to simulate and predict land subsidence. In this study, a decoupled three-dimensional (3-D) finite element land subsidence model including a 3-D ground water flow model and a 3-D geo-mechanical model was developed to simulate the 3-D deformation of the aquifer systems in the center area of Shanghai. The area of downtown Shanghai is 660 km2, with 10 million inhabitants, dense high buildings, and 11 metro lines. The simulation spans the period from 1979 to 1995. Two different assumptions have been tested on the side boundary, i.e., precluding the three components of the displacement, or assuming a free-displacement condition. The distribution of calculated land subsidence and horizontal displacements in different aquifers was analyzed. The computed vertical displacement fitted well with the available observations. It has been verified that the two different assumptions on the lateral boundaries in the geo-mechanical model caused different results just limited on nodes close to boundary. The developed 3-D land subsidence model is reasonable and can be used to simulate and predict 3-D movement of aquifer systems in the center area of Shanghai, which could provide scientific support to local government in controlling land subsidence and differential movements of the land surface.

  11. A Three-Dimensional Model of the Yeast Genome

    NASA Astrophysics Data System (ADS)

    Noble, William; Duan, Zhi-Jun; Andronescu, Mirela; Schutz, Kevin; McIlwain, Sean; Kim, Yoo Jung; Lee, Choli; Shendure, Jay; Fields, Stanley; Blau, C. Anthony

    Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase chromosomes are not positioned randomly within the nucleus, but instead adopt preferred conformations. Disparate DNA elements co-localize into functionally defined aggregates or factories for transcription and DNA replication. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among transfer RNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

  12. Three-dimensional parabolic equation modeling of mesoscale eddy deflection.

    PubMed

    Heaney, Kevin D; Campbell, Richard L

    2016-02-01

    The impact of mesoscale oceanography, including ocean fronts and eddies, on global scale low-frequency acoustics is examined using a fully three-dimensional parabolic equation model. The narrowband acoustic signal, for frequencies from 2 to 16 Hz, is simulated from a seismic event on the Kerguellen Plateau in the South Indian Ocean to an array of receivers south of Ascension Island in the South Atlantic, a distance of 9100 km. The path was chosen for its relevance to seismic detections from the HA10 Ascension Island station of the International Monitoring System, for its lack of bathymetric interaction, and for the dynamic oceanography encountered as the sound passes the Cape of Good Hope. The acoustic field was propagated through two years (1992 and 1993) of the eddy-permitting ocean state estimation ECCO2 (Estimating the Circulation and Climate of the Ocean, Phase II) system. The range of deflection of the back-azimuth was 1.8° with a root-mean-square of 0.34°. The refraction due to mesoscale oceanography could therefore have significant impacts upon localization of distant low-frequency sources, such as seismic or nuclear test events.

  13. Three-Dimensional Tissue Models of Normal and Diseased Skin

    PubMed Central

    Carlson, Mark W.; Alt-Holland, Addy; Egles, Christophe; Garlick, Jonathan A.

    2010-01-01

    Over the last decade, the development of in vitro, human, three-dimensional (3D) tissue models, known as human skin equivalents (HSEs), has furthered understanding of epidermal cell biology and provided novel experimental systems. Signaling pathways that mediate the linkage between growth and differentiation function optimally when cells are spatially organized to display the architectural features seen in vivo, but are uncoupled and lost in two-dimensional culture systems. HSEs consist of a stratified squamous epithelium grown at an air-liquid interface on a collagen matrix populated with dermal fibroblasts. These 3D tissues demonstrate in vivo–like epithelial differentiation and morphology, and rates of cell division, similar to those found in human skin. This unit describes fabrication of HSEs, allowing the generation of human tissues that mimic the morphology, differentiation, and growth of human skin, as well as disease processes of cancer and wound re-epithelialization, providing powerful new tools for the study of diseases in humans. PMID:19085986

  14. A Three-Dimensional Unsteady CFD Model of Compressor Stability

    NASA Technical Reports Server (NTRS)

    Chima, Rodrick V.

    2006-01-01

    A three-dimensional unsteady CFD code called CSTALL has been developed and used to investigate compressor stability. The code solved the Euler equations through the entire annulus and all blade rows. Blade row turning, losses, and deviation were modeled using body force terms which required input data at stations between blade rows. The input data was calculated using a separate Navier-Stokes turbomachinery analysis code run at one operating point near stall, and was scaled to other operating points using overall characteristic maps. No information about the stalled characteristic was used. CSTALL was run in a 2-D throughflow mode for very fast calculations of operating maps and estimation of stall points. Calculated pressure ratio characteristics for NASA stage 35 agreed well with experimental data, and results with inlet radial distortion showed the expected loss of range. CSTALL was also run in a 3-D mode to investigate inlet circumferential distortion. Calculated operating maps for stage 35 with 120 degree distortion screens showed a loss in range and pressure rise. Unsteady calculations showed rotating stall with two part-span stall cells. The paper describes the body force formulation in detail, examines the computed results, and concludes with observations about the code.

  15. A Three-Dimensional Model of the Yeast Genome

    PubMed Central

    Duan, Zhijun; Andronescu, Mirela; Schutz, Kevin; Mcllwain, Sean; Kim, Yoo Jung; Lee, Choli; Shendure, Jay; Fields, Stanley; Blau, C. Anthony; Noble, William S.

    2010-01-01

    Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes1-3. Interphase chromosomes are not positioned randomly within the nucleus but instead adopt preferred conformations4-7. Disparate DNA elements co-localize into functionally defined aggregates or “factories” for transcription8 and DNA replication9. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope10-12. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among tRNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome. PMID:20436457

  16. A three-dimensional ring current decay model

    NASA Technical Reports Server (NTRS)

    Fok, Mei-Ching; Moore, Thomas E.; Kozyra, Janet U.; Ho, George C.; Hamilton, Douglas C.

    1994-01-01

    This work is an extension of a previous ring current decay model. In the previous work, a two-dimensional kinetic model was constructed to study the temporal variations of the equatorially mirroring ring current ions, considering charge exchange and Coulomb drag losses along drift paths in a magnetic dipole field. In this work, particles with arbitrary pitch angle are considered. By bounce averaging the kinetic equation of the phase space density, information along magnetic field lines can be inferred from the equator. The three-dimensional model is used to simulate the recovery phase of a model great magnetic storm, similar to that which occurred in early February 1986. The initial distribution of ring current ions (at the minimum Dst) is extrapolated to all local times from AMPTE/CCE spacecraft observations on the dawn and dusk sides of the inner magnetosphere spanning the L value range L = 2.25 to 6.75. Observations by AMPTE/CCE of ring current distributions over subsequent orbits during the storm recovery phase are compared to model outputs. In general, the calculated ion fluxes are consistent with observations, except for H+ fluxes at tens of keV, which are always over-estimated. A newly-invented visualization idea, designated as a chromogram, is used to display the spatial and energy dependence of the ring current ion differential flux. Important features of storm-time ring current, such as day-night asymmetry during injection and drift hole on the dayside at low energies (less than 10 keV), are manifested in the chromogram representation. The pitch angle distribution is well fit by the function, j(sub o)(1+Ay(exp n)), where y is sine of the equatorial pitch angle. The evolution of the index n is a combined effect of charge exchange loss and particle drift. At low energies (less than 30 keV), both drift dispersion and charge exchange are important in determining n.

  17. A regional adaptive and assimilative three-dimensional ionospheric model

    NASA Astrophysics Data System (ADS)

    Sabbagh, Dario; Scotto, Carlo; Sgrigna, Vittorio

    2016-03-01

    A regional adaptive and assimilative three-dimensional (3D) ionospheric model is proposed. It is able to ingest real-time data from different ionosondes, providing the ionospheric bottomside plasma frequency fp over the Italian area. The model is constructed on the basis of empirical values for a set of ionospheric parameters Pi[base] over the considered region, some of which have an assigned variation ΔPi. The values for the ionospheric parameters actually observed at a given time at a given site will thus be Pi = Pi[base] + ΔPi. These Pi values are used as input for an electron density N(h) profiler. The latter is derived from the Advanced Ionospheric Profiler (AIP), which is software used by Autoscala as part of the process of automatic inversion of ionogram traces. The 3D model ingests ionosonde data by minimizing the root-mean-square deviation between the observed and modeled values of fp(h) profiles obtained from the associated N(h) values at the points where observations are available. The ΔPi values are obtained from this minimization procedure. The 3D model is tested using data collected at the ionospheric stations of Rome (41.8N, 12.5E) and Gibilmanna (37.9N, 14.0E), and then comparing the results against data from the ionospheric station of San Vito dei Normanni (40.6N, 18.0E). The software developed is able to produce maps of the critical frequencies foF2 and foF1, and of fp at a fixed altitude, with transverse and longitudinal cross-sections of the bottomside ionosphere in a color scale. fp(h) and associated simulated ordinary ionogram traces can easily be produced for any geographic location within the Italian region. fp values within the volume in question can also be provided.

  18. Fully three-dimensional simulation and modeling of a dense plasma focus

    SciTech Connect

    Meehan, B. T.; Niederhaus, J. H. J.

    2014-10-01

    A dense plasma focus (DPF) is a pulsed-power machine that electromagnetically accelerates and cylindrically compresses a shocked plasma in a Z-pinch. The pinch results in a brief (~ 100 ns) pulse of X-rays, and, for some working gases, also a pulse of neutrons. A great deal of experimental research has been done into the physics of DPF reactions, and there exist mathematical models describing its behavior during the different time phases of the reaction. Two of the phases, known as the inverse pinch and the rundown, are approximately governed by magnetohydrodynamics, and there are a number of well-established codes for simulating these phases in two dimensions or in three dimensions under the assumption of axial symmetry. There has been little success, however, in developing fully three-dimensional simulations. In this work we present three-dimensional simulations of DPF reactions and demonstrate that three-dimensional simulations predict qualitatively and quantitatively different behavior than their two-dimensional counterparts. One of the most important quantities to predict is the time duration between the formation of the gas shock and Z-pinch, and the three-dimensional simulations more faithfully represent experimental results for this time duration and are essential for accurate prediction of future experiments.

  19. Three dimensional modeling of Laser-Plasma interaction: benchmarking our predictive modeling tools vs. experiments

    SciTech Connect

    Divol, L; Berger, R; Meezan, N; Froula, D H; Dixit, S; Suter, L; Glenzer, S H

    2007-11-08

    We have developed a new target platform to study Laser Plasma Interaction in ignition-relevant condition at the Omega laser facility (LLE/Rochester)[1]. By shooting an interaction beam along the axis of a gas-filled hohlraum heated by up to 17 kJ of heater beam energy, we were able to create a millimeter-scale underdense uniform plasma at electron temperatures above 3 keV. Extensive Thomson scattering measurements allowed us to benchmark our hydrodynamic simulations performed with HYDRA[2]. As a result of this effort, we can use with much confidence these simulations as input parameters for our LPI simulation code pF3d[3]. In this paper, we show that by using accurate hydrodynamic profiles and full three-dimensional simulations including a realistic modeling of the laser intensity pattern generated by various smoothing options, whole beam three-dimensional linear kinetic modeling of stimulated Brillouin scattering reproduces quantitatively the experimental measurements(SBS thresholds, reflectivity values and the absence of measurable SRS). This good agreement was made possible by the recent increase in computing power routinely available for such simulations. These simulations accurately predicted the strong reduction of SBS measured when polarization smoothing is used.

  20. Three-dimensional modeling of laser-plasma interaction: Benchmarking our predictive modeling tools versus experiments

    SciTech Connect

    Divol, L.; Berger, R. L.; Meezan, N. B.; Froula, D. H.; Dixit, S.; Michel, P.; London, R.; Strozzi, D.; Ross, J.; Williams, E. A.; Still, B.; Suter, L. J.; Glenzer, S. H.

    2008-05-15

    New experimental capabilities [Froula et al., Phys. Rev. Lett. 98, 085001 (2007)] have been developed to study laser-plasma interaction (LPI) in ignition-relevant condition at the Omega laser facility (LLE/Rochester). By shooting an interaction beam along the axis of a gas-filled hohlraum heated by up to 17 kJ of heater beam energy, a millimeter-scale underdense uniform plasma at electron temperatures above 3 keV was created. Extensive Thomson scattering measurements allowed to benchmark hydrodynamic simulations performed with HYDRA [Meezan et al., Phys. Plasmas 14, 056304 (2007)]. As a result of this effort, these simulations can be used with much confidence as input parameters for the LPI simulation code PF3D [Berger et al., Phys. Plasmas 5, 4337 (1998)]. In this paper, it is shown that by using accurate hydrodynamic profiles and full three-dimensional simulations including a realistic modeling of the laser intensity pattern generated by various smoothing options, whole beam three-dimensional linear kinetic modeling of stimulated Brillouin scattering (SBS) reproduces quantitatively the experimental measurements (SBS thresholds, reflectivity values, and the absence of measurable stimulated Raman scattering). This good agreement was made possible by the recent increase in computing power routinely available for such simulations. These simulations accurately predicted the strong reduction of SBS measured when polarization smoothing is used.

  1. A multiphase model for three-dimensional tumor growth

    NASA Astrophysics Data System (ADS)

    Sciumè, G.; Shelton, S.; Gray, W. G.; Miller, C. T.; Hussain, F.; Ferrari, M.; Decuzzi, P.; Schrefler, B. A.

    2013-01-01

    infiltration is predicted for the opposite condition. Interestingly, the infiltration potential of the tumor mass is mostly driven by the relative cell adhesion to the ECM. In the third case, a tumor cord model is analyzed where the malignant cells grow around microvessels in a three-dimensional geometry. It is shown that TCs tend to migrate among adjacent vessels seeking new oxygen and nutrients. This model can predict and optimize the efficacy of anticancer therapeutic strategies. It can be further developed to answer questions on tumor biophysics, related to the effects of ECM stiffness and cell adhesion on TC proliferation.

  2. Three-dimensional Thermal Model of the Mexican Subduction Zone

    NASA Astrophysics Data System (ADS)

    Rosas, J. C.; Pimentel, F. D. C.; Currie, C. A.; He, J.; Harris, R. N.

    2015-12-01

    Along the Mexican section of the Middle America Trench (MAT), the Cocos plate subducts beneath the North American plate. The most important feature of this subduction zone is the flat-slab section below central Mexico, extending approximately 250 km landward from the trench at a depth of 50 km. Further west, the dip changes to 45-50º. This particular geometry has several unique consequences, such as a volcanic arc that is not aligned with the trench and very shallow slab seismicity. For the mantle wedge, the abrupt change in slab geometry could lead to a three-dimensional (3D) mantle wedge flow that departs from the classical 2D subduction-driven corner flow. Evidence of 3D flow in the region comes from seismic anisotropy studies, which show that olivine fast-direction axes have a component that is parallel to the MAT. In other subduction zones, such as Costa Rica-Nicaragua and Japan, 3D flow has been observed to increase temperatures by >50º C relative to corner flow models.For this study, we have created the first 3D finite-element model of the Mexican subduction zone in order to analyze its thermal structure. Our objective is to assess the effects of 3D mantle flow and hydrothermal circulation (HC) in the subducting slab. In this region, low surface heat flow values near the trench indicate that HC may remove heat from the oceanic plate. Our model incorporates the effect of HC through conductivity proxies in the subducting crust and a 2D oceanic geotherm that includes the age variations of the Cocos plate along the MAT. For an isoviscous mantle, our model shows that the slab dip variations induce a flow that departs from 2D corner flow near the transition between the flat-slab and normal-dipping sections. The mantle flows in eastward direction toward the flat slab, and its orientation is consistent with seismic anisotropy studies. The maximum along-margin flow rate is nearly 2 cm/yr, which is >30% of the convergence rate. Temperatures at the location of this

  3. Accurate three-dimensional virtual reconstruction of surgical field using calibrated trajectories of an image-guided medical robot

    PubMed Central

    Gong, Yuanzheng; Hu, Danying; Hannaford, Blake; Seibel, Eric J.

    2014-01-01

    Abstract. Brain tumor margin removal is challenging because diseased tissue is often visually indistinguishable from healthy tissue. Leaving residual tumor leads to decreased survival, and removing normal tissue causes life-long neurological deficits. Thus, a surgical robotics system with a high degree of dexterity, accurate navigation, and highly precise resection is an ideal candidate for image-guided removal of fluorescently labeled brain tumor cells. To image, we developed a scanning fiber endoscope (SFE) which acquires concurrent reflectance and fluorescence wide-field images at a high resolution. This miniature flexible endoscope was affixed to the arm of a RAVEN II surgical robot providing programmable motion with feedback control using stereo-pair surveillance cameras. To verify the accuracy of the three-dimensional (3-D) reconstructed surgical field, a multimodal physical-sized model of debulked brain tumor was used to obtain the 3-D locations of residual tumor for robotic path planning to remove fluorescent cells. Such reconstruction is repeated intraoperatively during margin clean-up so the algorithm efficiency and accuracy are important to the robotically assisted surgery. Experimental results indicate that the time for creating this 3-D surface can be reduced to one-third by using known trajectories of a robot arm, and the error from the reconstructed phantom is within 0.67 mm in average compared to the model design. PMID:26158071

  4. Accurate three-dimensional virtual reconstruction of surgical field using calibrated trajectories of an image-guided medical robot.

    PubMed

    Gong, Yuanzheng; Hu, Danying; Hannaford, Blake; Seibel, Eric J

    2014-10-01

    Brain tumor margin removal is challenging because diseased tissue is often visually indistinguishable from healthy tissue. Leaving residual tumor leads to decreased survival, and removing normal tissue causes life-long neurological deficits. Thus, a surgical robotics system with a high degree of dexterity, accurate navigation, and highly precise resection is an ideal candidate for image-guided removal of fluorescently labeled brain tumor cells. To image, we developed a scanning fiber endoscope (SFE) which acquires concurrent reflectance and fluorescence wide-field images at a high resolution. This miniature flexible endoscope was affixed to the arm of a RAVEN II surgical robot providing programmable motion with feedback control using stereo-pair surveillance cameras. To verify the accuracy of the three-dimensional (3-D) reconstructed surgical field, a multimodal physical-sized model of debulked brain tumor was used to obtain the 3-D locations of residual tumor for robotic path planning to remove fluorescent cells. Such reconstruction is repeated intraoperatively during margin clean-up so the algorithm efficiency and accuracy are important to the robotically assisted surgery. Experimental results indicate that the time for creating this 3-D surface can be reduced to one-third by using known trajectories of a robot arm, and the error from the reconstructed phantom is within 0.67 mm in average compared to the model design.

  5. A comparison of two- and three-dimensional stochastic models of regional solute movement

    USGS Publications Warehouse

    Shapiro, A.M.; Cvetkovic, V.D.

    1990-01-01

    Recent models of solute movement in porous media that are based on a stochastic description of the porous medium properties have been dedicated primarily to a three-dimensional interpretation of solute movement. In many practical problems, however, it is more convenient and consistent with measuring techniques to consider flow and solute transport as an areal, two-dimensional phenomenon. The physics of solute movement, however, is dependent on the three-dimensional heterogeneity in the formation. A comparison of two- and three-dimensional stochastic interpretations of solute movement in a porous medium having a statistically isotropic hydraulic conductivity field is investigated. To provide an equitable comparison between the two- and three-dimensional analyses, the stochastic properties of the transmissivity are defined in terms of the stochastic properties of the hydraulic conductivity. The variance of the transmissivity is shown to be significantly reduced in comparison to that of the hydraulic conductivity, and the transmissivity is spatially correlated over larger distances. These factors influence the two-dimensional interpretations of solute movement by underestimating the longitudinal and transverse growth of the solute plume in comparison to its description as a three-dimensional phenomenon. Although this analysis is based on small perturbation approximations and the special case of a statistically isotropic hydraulic conductivity field, it casts doubt on the use of a stochastic interpretation of the transmissivity in describing regional scale movement. However, by assuming the transmissivity to be the vertical integration of the hydraulic conductivity field at a given position, the stochastic properties of the hydraulic conductivity can be estimated from the stochastic properties of the transmissivity and applied to obtain a more accurate interpretation of solute movement. ?? 1990 Kluwer Academic Publishers.

  6. Three-dimensional bioremediation modeling in heterogeneous porous media

    SciTech Connect

    Wheeler, M.F.; Roberson, K.R.; Chilakapati, A.

    1992-06-01

    Recently Price University and Pacific Northwest Laboratory (PNL) have begun a collaborative research effort that involves laboratory, field, and simulation work directed toward validating remediation strategies, including both natural and in situ bioremediation at US Department of Energy (DOE) sites such as Hanford. Because of chemical, biological, geologic and physical complexities of modeling these DOE sites, one of the major simulation goals of the project is to formulate and implement accurate and efficient (parallel) algorithms for modeling multiphase/multicomponent mow and reactive transport. In this paper we first describe the physical problem that needs to be modeled. Because of the emergence of concurrent supercomputing, we propose accurate numerical algorithms that are based on operator-splitting in time and domain decomposition iterative techniques. In particular reference is made to the biodegradation of carbon tetrachloride.

  7. Three-dimensional modelling in magnetotelluric and magnetic variational sounding

    NASA Technical Reports Server (NTRS)

    Reddy, I. K.; Phillips, R. J.; Rankin, D.

    1977-01-01

    The Galerkin finite-element method is used to obtain approximate solutions for the three-dimensional induction problem. A rectangular conductive prism is considered as an example, and solutions are obtained for linear and circularly polarized incident plane-wave fields. Magnetotelluric tensor impedances and magnetic transfer functions are computed. Polar diagrams of the tensor impedances and magnetic transfer functions along with their amplitude contour maps are presented. The dimensionality parameter, skew, is contoured at the surface of the earth. It is shown that the relative amplitudes and shapes of the additional and principal impedance polar diagrams can be used to determine the dimensionality of geoelectrical structures. Stations with skew values greater than 0.2 are significantly influenced by the three-dimensionality of the geoelectric structure. The amplitudes of the magnetic transfer function and the orientations of its polar diagrams exhibit large anomalies in the vicinity of the intersection of the lateral contacts.

  8. Three-dimensional finite element modeling of liquid crystal devices

    NASA Astrophysics Data System (ADS)

    Vanbrabant, Pieter J. M.; James, Richard; Beeckman, Jeroen; Neyts, Kristiaan; Willman, Eero; Fernandez, F. Anibal

    2011-03-01

    A finite element framework is presented to combine advanced three-dimensional liquid crystal director calculations with a full-vector beam propagation analysis. This approach becomes especially valuable to analyze and design structures in which disclinations or diffraction effects play an important role. The wide applicability of the approach is illustrated in our overview from several examples including small pixel LCOS microdisplays with homeotropic alignment.

  9. Solution of the surface Euler equations for accurate three-dimensional boundary-layer analysis of aerodynamic configurations

    NASA Technical Reports Server (NTRS)

    Iyer, V.; Harris, J. E.

    1987-01-01

    The three-dimensional boundary-layer equations in the limit as the normal coordinate tends to infinity are called the surface Euler equations. The present paper describes an accurate method for generating edge conditions for three-dimensional boundary-layer codes using these equations. The inviscid pressure distribution is first interpolated to the boundary-layer grid. The surface Euler equations are then solved with this pressure field and a prescribed set of initial and boundary conditions to yield the velocities along the two surface coordinate directions. Results for typical wing and fuselage geometries are presented. The smoothness and accuracy of the edge conditions obtained are found to be superior to the conventional interpolation procedures.

  10. Three dimensional gravity field modelling of the Chicxulub impact crater

    NASA Astrophysics Data System (ADS)

    Hildebrand, A.; Millar, J.; Pilkington, M.; Lawton, D.

    2003-04-01

    Three dimensional gravity field modeling of the Chicxulub crater’s gravity field has refined our working structural model [e.g. 1, 2], and differs somewhat from the results of [3]. The 3D gravity model establishes that the central uplift is within reach of scientific drilling. The 3D gravity modeling method employed is that of [4]. Modelling results particularly reveal the crater’s central structures. The central uplift is a twin peaked structural high with vergence towards the southwest as previously indicated by 2D models [1] and consistent with seismic refraction results [5]. An arm extends towards the northeast, in contrast to the steep gradients that bound the central uplift to the southwest. The width of the uplift at 4 km depth is ~45 km broadening to ~60 km at 5 km depth consistent with 2D modeling. The central uplift rises into the melt sheet to ~2 km depth in contrast to the results of [4] where a top of ~4 km was obtained. However, as refraction results [5] independently constrain the central uplift width and the central uplift density contrast is limited (+0.11gcm-3 here), this is probably a realistic result. The shape of the modeled central uplift is radically different from that advocated by [6] who, based on seismic refraction results, proposed a cup-shaped central uplift (concave top) with a top at ~3 km depth, but of similar width. This interpretation requires substantial departure from density velocity proportionality, and we doubt that the central uplift has an annular top. The filling of the CDC, which we interpret as melt, is revealed as a body slightly elongated in a NE-SW sense with a size consistent with previous 2D model results. With the density contrast measured from the top of the melt sheet, its base lies near ~4 km is obtained consistent with the result of [4]. This depth is dependent upon the density contrast used (-0.15 g/cc), however, and all the mass deficiency need not be melt. The derived melt volume is 1.5 X 104 km3

  11. Three dimensional accurate morphology measurements of polystyrene standard particles on silicon substrate by electron tomography.

    PubMed

    Hayashida, Misa; Kumagai, Kazuhiro; Malac, Marek

    2015-12-01

    Polystyrene latex (PSL) nanoparticle (NP) sample is one of the most widely used standard materials. It is used for calibration of particle counters and particle size measurement tools. It has been reported that the measured NP sizes by various methods, such as Differential Mobility Analysis, dynamic light scattering (DLS), optical microscopy (OM), scanning electron microscopy (SEM) and atomic force microscopy (AFM), differ from each other. Deformation of PSL NPs on mica substrate has been reported in AFM measurements: the lateral width of PSL NPs is smaller than their vertical height. To provide a reliable calibration standard, the deformation must be measured by a method that can reliably visualize the entire three dimensional (3D) shape of the PSL NPs. Here we present a method for detailed measurement of PSL NP 3D shape by means of electron tomography in a transmission electron microscope. The observed shape of the PSL NPs with 100 nm and 50 nm diameter were not spherical, but squished in direction perpendicular to the support substrate by about 7.4% and 12.1%, respectively. The high difference in surface energy of the PSL NPs and that of substrate together with their low Young modulus appear to explain the squishing of the NPs without presence of water film.

  12. Errors between two- and three-dimensional thermal model predictions of hyperthermia treatments.

    PubMed

    Chen, Z P; Miller, W H; Roemer, R B; Cetas, T C

    1990-01-01

    A simulation program to study the three-dimensional temperature distributions produced by hyperthermia in anatomically realistic inhomogenous tissue models has been developed using the bioheat transfer equation. The anatomical data for the inhomogeneous tissues of the human body are entered on a digitizing tablet from serial computed tomography (CT) scans. Power deposition patterns from various heating modalities must be calculated independently. The program has been used to comparatively evaluate two- and three-dimensional simulations in a series of parametric calculations based on a simple inhomogeneous tissue model for uniform power deposition. The conclusions are that two-dimensional simulations always lead to significant errors at the ends of tumors (up to tens of degrees). However, they can give valid results for the central region of large tumors, but only with tumor blood perfusions greater than approximately 1 kg/m3/s. These conclusions from the geometrically simple model are substantiated by the results obtained using the full three-dimensional model for actual patient anatomical simulations. In summary, three-dimensional simulations will be necessary for accurate patient treatment planning. The effect of the thermal conductivity, used in the models, on the temperature field has also been studied. The results show that using any thermal conductivity value in the range of 0.4 to 0.6 W/m/degrees C sufficiently characterizes most soft tissues, especially in the presence of high blood perfusion. However, bone (thermal conductivity of 1.16 W/m/degrees C) and fat (thermal conductivity of 0.2 W/m/degrees C) do not fit this generalization and significant errors result if soft tissue values are used.

  13. Mass Spectrometry Imaging of Therapeutics from Animal Models to Three-Dimensional Cell Cultures

    PubMed Central

    Liu, Xin; Hummon, Amanda B.

    2016-01-01

    Mass spectrometry imaging (MSI) is a powerful label-free technique for the investigation of the spatial distribution of molecules at complex surfaces and has been widely used in the pharmaceutical sciences to understand the distribution of different drugs and their metabolites in various biological samples, ranging from cell-based models to tissues. Here, we review the current applications of MSI for drug studies in animal models, followed by a discussion of the novel advances of MSI in three-dimensional (3D) cell cultures for accurate, efficient and high-throughput analyses to evaluate therapeutics. PMID:26084404

  14. Three-dimensional hydrodynamic and erosion modeling of fluidized beds using kinetic theory

    SciTech Connect

    Ding, J.; Lyczkowski, R.W. ); Burge, S.W. . Research Center)

    1992-05-01

    Three-dimensional hydrodynamic models for gas-solids flow are developed and used to compute bubble and solids motion in rectangular fluidized beds. Our computed results demonstrate the significance and necessity for three-dimensional models of hydrodynamics and erosion in fluidized-bed combustors. A kinetic theory model for erosion using Finnie's single-particle ductile erosion model was used to compute erosion in a rectangular fluidized bed containing a single tube. Comparison of two-dimensional and three-dimensional computed hydrodynamics, erosion rates, and patterns clearly show the superiority of three-dimensional modeling.

  15. Three-dimensional hydrodynamic and erosion modeling of fluidized beds using kinetic theory

    SciTech Connect

    Ding, J.; Lyczkowski, R.W.; Burge, S.W.

    1992-05-01

    Three-dimensional hydrodynamic models for gas-solids flow are developed and used to compute bubble and solids motion in rectangular fluidized beds. Our computed results demonstrate the significance and necessity for three-dimensional models of hydrodynamics and erosion in fluidized-bed combustors. A kinetic theory model for erosion using Finnie`s single-particle ductile erosion model was used to compute erosion in a rectangular fluidized bed containing a single tube. Comparison of two-dimensional and three-dimensional computed hydrodynamics, erosion rates, and patterns clearly show the superiority of three-dimensional modeling.

  16. Three-dimensional numerical modeling of indium phosphide Point-Contact Solar Cells

    NASA Technical Reports Server (NTRS)

    Clark, Ralph O.

    1992-01-01

    The Point-Contact Solar Cell (PCSC) geometry has proven very effective for silicon cells. To date, it has not been implemented in III-V materials. In addition, modeling such a geometry is very difficult because of its three-dimensional nature. We have developed a three-dimensional finite element modeling code (FIESTA ROC). In this paper, we present results from a three-dimensional modeling study of InP point-contact solar cells.

  17. Technical Note: PRESAGE three-dimensional dosimetry accurately measures Gamma Knife output factors

    PubMed Central

    Klawikowski, Slade J.; Yang, James N.; Adamovics, John; Ibbott, Geoffrey S.

    2014-01-01

    Small-field output factor measurements are traditionally very difficult because of steep dose gradients, loss of lateral electronic equilibrium, and dose volume averaging in finitely sized detectors. Three-dimensional (3D) dosimetry is ideal for measuring small output factors and avoids many of these potential challenges of point and two-dimensional detectors. PRESAGE 3D polymer dosimeters were used to measure the output factors for the 4 mm and 8 mm collimators of the Leksell Perfexion Gamma Knife radiosurgery treatment system. Discrepancies between the planned and measured distance between shot centers were also investigated. A Gamma Knife head frame was mounted onto an anthropomorphic head phantom. Special inserts were machined to hold 60 mm diameter, 70 mm tall cylindrical PRESAGE dosimeters. The phantom was irradiated with one 16 mm shot and either one 4 mm or one 8 mm shot, to a prescribed dose of either 3 Gy or 4 Gy to the 50% isodose line. The two shots were spaced between 30 mm and 60 mm apart and aligned along the central axis of the cylinder. The Presage dosimeters were measured using the DMOS-RPC optical CT scanning system. Five independent 4 mm output factor measurements fell within 2% of the manufacturer’s Monte Carlo simulation-derived nominal value, as did two independent 8 mm output factor measurements. The measured distances between shot centers varied by ± 0.8 mm with respect to the planned shot displacements. On the basis of these results, we conclude that PRESAGE dosimetry is excellently suited to quantify the difficult-to-measure Gamma Knife output factors. PMID:25368961

  18. Three-dimensional conceptual model for the Hanford Site unconfined aquifer system: FY 1994 status report

    SciTech Connect

    Thorne, P.D.; Chamness, M.A.; Vermeul, V.R.; Macdonald, Q.C.; Schubert, S.E.

    1994-11-01

    This report documents work conducted during the fiscal year 1994 to development an improved three-dimensional conceptual model of ground-water flow in the unconfined aquifer system across the Hanford Site Ground-Water Surveillance Project, which is managed by Pacific Northwest Laboratory. The main objective of the ongoing effort to develop an improved conceptual model of ground-water flow is to provide the basis for improved numerical report models that will be capable of accurately predicting the movement of radioactive and chemical contaminant plumes in the aquifer beneath Hanford. More accurate ground-water flow models will also be useful in assessing the impacts of changes in facilities and operations. For example, decreasing volumes of operational waste-water discharge are resulting in a declining water table in parts of the unconfined aquifer. In addition to supporting numerical modeling, the conceptual model also provides a qualitative understanding of the movement of ground water and contaminants in the aquifer.

  19. Predictive three dimensional modeling of Stimulated Brillouin Scattering in ignition-scale experiments

    SciTech Connect

    Divol, L; Berger, R; Meezan, N; Froula, D H; Dixit, S; Suter, L; Glenzer, S H

    2007-11-07

    The first three-dimensional (3D) simulations of a high power 0.351 {micro}m laser beam propagating through a high temperature hohlraum plasma are reported. We show that 3D linear kinetic modeling of Stimulated Brillouin scattering reproduces quantitatively the experimental measurements, provided it is coupled to detailed hydrodynamics simulation and a realistic description of the laser beam from its millimeter-size envelop down to the micron scale speckles. These simulations accurately predict the strong reduction of SBS measured when polarization smoothing is used.

  20. Hydrogen program combustion research: Three dimensional computational modeling

    SciTech Connect

    Johnson, N.L.; Amsden, A.A.; Butler, T.D.

    1995-05-01

    We have significantly increased our computational modeling capability by the addition of a vertical valve model in KIVA-3, code used internationally for engine design. In this report the implementation and application of the valve model is described. The model is shown to reproduce the experimentally verified intake flow problem examined by Hessel. Furthermore, the sensitivity and performance of the model is examined for the geometry and conditions of the hydrogen-fueled Onan engine in development at Sandia National Laboratory. Overall the valve model is shown to have comparable accuracy as the general flow simulation capability in KIVA-3, which has been well validated by past comparisons to experiments. In the exploratory simulations of the Onan engine, the standard use of the single kinetic reaction for hydrogen oxidation was found to be inadequate for modeling the hydrogen combustion because of its inability to describe both the observed laminar flame speed and the absence of autoignition in the Onan engine. We propose a temporary solution that inhibits the autoignition without sacrificing the ability to model spark ignition. In the absence of experimental data on the Onan engine, a computational investigation was undertaken to evaluate the importance of modeling the intake flow on the combustion and NO{sub x} emissions. A simulation that began with the compression of a quiescent hydrogen-air mixture was compared to a simulation of the full induction process with resolved opening and closing of the intake valve. Although minor differences were observed in the cylinder-averaged pressure, temperature, bulk-flow kinetic energy and turbulent kinetic energy, large differences where observed in the hydrogen combustion rate and NO{sub x} emissions. The flow state at combustion is highly heterogeneous and sensitive to the details of the bulk and turbulent flow and that an accurate simulation of the Onan engine must include the modeling of the air-fuel induction.

  1. Accuracy of three-dimensional, paper-based models generated using a low-cost, three-dimensional printer.

    PubMed

    Olszewski, Raphael; Szymor, Piotr; Kozakiewicz, Marcin

    2014-12-01

    Our study aimed to determine the accuracy of a low-cost, paper-based 3D printer by comparing a dry human mandible to its corresponding three-dimensional (3D) model using a 3D measuring arm. One dry human mandible and its corresponding printed model were evaluated. The model was produced using DICOM data from cone beam computed tomography. The data were imported into Maxilim software, wherein automatic segmentation was performed, and the STL file was saved. These data were subsequently analysed, repaired, cut and prepared for printing with netfabb software. These prepared data were used to create a paper-based model of a mandible with an MCor Matrix 300 printer. Seventy-six anatomical landmarks were chosen and measured 20 times on the mandible and the model using a MicroScribe G2X 3D measuring arm. The distances between all the selected landmarks were measured and compared. Only landmarks with a point inaccuracy less than 30% were used in further analyses. The mean absolute difference for the selected 2016 measurements was 0.36 ± 0.29 mm. The mean relative difference was 1.87 ± 3.14%; however, the measurement length significantly influenced the relative difference. The accuracy of the 3D model printed using the paper-based, low-cost 3D Matrix 300 printer was acceptable. The average error was no greater than that measured with other types of 3D printers. The mean relative difference should not be considered the best way to compare studies. The point inaccuracy methodology proposed in this study may be helpful in future studies concerned with evaluating the accuracy of 3D rapid prototyping models.

  2. LEGEND - a three-dimensional LEO-to-GEO debris evolutionary model

    NASA Astrophysics Data System (ADS)

    Liou, J.-C.; Hall, D. T.; Krisko, P. H.; Opiela, J. N.

    2004-01-01

    A new orbital debris evolutionary model is being developed by the NASA Orbital Debris Program Office at Johnson Space Center. LEGEND, a LEO-to-GEO Environment Debris model, is capable of reproducing the historical debris environment as well as performing future debris environment projection. The model covers the near Earth space between 200 and 40,000 km altitude and outputs debris distributions in one-dimensional (altitude), two-dimensional (altitude, latitude), and three-dimensional (altitude, latitude, longitude) formats. LEGEND is a three-year (2001-2003) project. The historical part of the model has been completed and the future projection part is being developed/tested. The model utilizes a recently updated historical satellite launch database, two efficient and accurate propagators, and a new NASA satellite breakup model. This paper summarizes the justifications for building a full-scale three-dimensional debris evolutionary model, the overall model structure, and several key components of the model. Preliminary model predictions of debris distributions in the Low Earth Orbit (LEO), Medium Earth Orbit (MEO), and Geosynchronous Earth Orbit (GEO) regions are presented.

  3. [Study on the methods for establishing virtual three-dimensional models of cerebral arteries with the three-dimensional moulding software].

    PubMed

    Wei, Xin; Xie, Xiaodong; Wang, Chaohua

    2007-12-01

    This study was conducted to establish the methods of virtual three-dimensional cerebral arteries models by use of three-dimensional moulding software. The virtual models of the cerebral arteries were established using the three-dimensional moulding software of 3D Studio MAX R3 with 46 cases of normal cerebral DSA image as the original. The results showed there was similarity in appearance between the virtual cerebral arteries and DSA image. This is of benefit to understanding the vascular three-dimensional spatial relation in visual sense. Several models of different variant anatomy could be easily established on the copy files of the virtual cerebral arteries model. The virtual model could help learners to create and increase the three-dimensional space concept of arteries and aneurysms in clinical teaching. The results indicated that the virtual three-dimensional cerebral arteries models could display the three-dimensional spatial relation of the cerebral arterial system distinctly, and could serve as a morphologic foundation in the researches on vascular disease. PMID:18232470

  4. Accurate Adaptive Level Set Method and Sharpening Technique for Three Dimensional Deforming Interfaces

    NASA Technical Reports Server (NTRS)

    Kim, Hyoungin; Liou, Meng-Sing

    2011-01-01

    In this paper, we demonstrate improved accuracy of the level set method for resolving deforming interfaces by proposing two key elements: (1) accurate level set solutions on adapted Cartesian grids by judiciously choosing interpolation polynomials in regions of different grid levels and (2) enhanced reinitialization by an interface sharpening procedure. The level set equation is solved using a fifth order WENO scheme or a second order central differencing scheme depending on availability of uniform stencils at each grid point. Grid adaptation criteria are determined so that the Hamiltonian functions at nodes adjacent to interfaces are always calculated by the fifth order WENO scheme. This selective usage between the fifth order WENO and second order central differencing schemes is confirmed to give more accurate results compared to those in literature for standard test problems. In order to further improve accuracy especially near thin filaments, we suggest an artificial sharpening method, which is in a similar form with the conventional re-initialization method but utilizes sign of curvature instead of sign of the level set function. Consequently, volume loss due to numerical dissipation on thin filaments is remarkably reduced for the test problems

  5. Fast and accurate finite element analysis of large-scale three-dimensional photonic devices with a robust domain decomposition method.

    PubMed

    Xue, Ming-Feng; Kang, Young Mo; Arbabi, Amir; McKeown, Steven J; Goddard, Lynford L; Jin, Jian-Ming

    2014-02-24

    A fast and accurate full-wave technique based on the dual-primal finite element tearing and interconnecting method and the second-order transmission condition is presented for large-scale three-dimensional photonic device simulations. The technique decomposes a general three-dimensional electromagnetic problem into smaller subdomain problems so that parallel computing can be performed on distributed-memory computer clusters to reduce the simulation time significantly. With the electric fields computed everywhere, photonic device parameters such as transmission and reflection coefficients are extracted. Several photonic devices, with simulation volumes up to 1.9×10(4) (λ/n(avg))3 and modeled with over one hundred million unknowns, are simulated to demonstrate the application, efficiency, and capability of this technique. The simulations show good agreement with experimental results and in a special case with a simplified two-dimensional simulation.

  6. Three-dimensional in vitro co-culture model of breast tumor using magnetic levitation.

    PubMed

    Jaganathan, Hamsa; Gage, Jacob; Leonard, Fransisca; Srinivasan, Srimeenakshi; Souza, Glauco R; Dave, Bhuvanesh; Godin, Biana

    2014-01-01

    In this study, we investigate a novel in vitro model to mimic heterogeneous breast tumors without the use of a scaffold while allowing for cell-cell and tumor-fibroblast interactions. Previous studies have shown that magnetic levitation system under conventional culturing conditions results in the formation of three-dimensional (3D) structures, closely resembling in vivo tissues (fat tissue, vasculature, etc.). Three-dimensional heterogeneous tumor models for breast cancer were designed to effectively model the influences of the tumor microenvironment on drug efficiency. Various breast cancer cells were co-cultured with fibroblasts and then magnetically levitated. Size and cell density of the resulting tumors were measured. The model was phenotypically compared to in vivo tumors and examined for the presence of ECM proteins. Lastly, the effects of tumor stroma in the 3D in vitro model on drug transport and efficiency were assessed. Our data suggest that the proposed 3D in vitro breast tumor is advantageous due to the ability to: (1) form large-sized (millimeter in diameter) breast tumor models within 24 h; (2) control tumor cell composition and density; (3) accurately mimic the in vivo tumor microenvironment; and (4) test drug efficiency in an in vitro model that is comparable to in vivo tumors. PMID:25270048

  7. A microfluidically perfused three dimensional human liver model.

    PubMed

    Rennert, Knut; Steinborn, Sandra; Gröger, Marko; Ungerböck, Birgit; Jank, Anne-Marie; Ehgartner, Josef; Nietzsche, Sandor; Dinger, Julia; Kiehntopf, Michael; Funke, Harald; Peters, Frank T; Lupp, Amelie; Gärtner, Claudia; Mayr, Torsten; Bauer, Michael; Huber, Otmar; Mosig, Alexander S

    2015-12-01

    Within the liver, non-parenchymal cells (NPCs) are critically involved in the regulation of hepatocyte polarization and maintenance of metabolic function. We here report the establishment of a liver organoid that integrates NPCs in a vascular layer composed of endothelial cells and tissue macrophages and a hepatic layer comprising stellate cells co-cultured with hepatocytes. The three-dimensional liver organoid is embedded in a microfluidically perfused biochip that enables sufficient nutrition supply and resembles morphological aspects of the human liver sinusoid. It utilizes a suspended membrane as a cell substrate mimicking the space of Disse. Luminescence-based sensor spots were integrated into the chip to allow online measurement of cellular oxygen consumption. Application of microfluidic flow induces defined expression of ZO-1, transferrin, ASGPR-1 along with an increased expression of MRP-2 transporter protein within the liver organoids. Moreover, perfusion was accompanied by an increased hepatobiliary secretion of 5(6)-carboxy-2',7'-dichlorofluorescein and an enhanced formation of hepatocyte microvilli. From this we conclude that the perfused liver organoid shares relevant morphological and functional characteristics with the human liver and represents a new in vitro research tool to study human hepatocellular physiology at the cellular level under conditions close to the physiological situation.

  8. Three-dimensional modelling of trace species in the Arctic lower stratosphere

    NASA Technical Reports Server (NTRS)

    Chipperfield, Martyn; Cariolle, Daniel; Simon, Pascal; Ramaroson, Richard

    1994-01-01

    A three-dimensional radiative-dynamical-chemical model has been developed and used to study some aspects of modeling the polar lower stratosphere. The model includes a comprehensive gas-phase chemistry scheme as well as a treatment of heterogeneous reactions occurring on the surface of polar stratospheric clouds. Tracer transport is treated by an accurate, nondispersive scheme with little diffusion suited to the representation of strong gradients. Results from a model simulation of early February 1990 are presented and used to illustrate the importance of the model transport scheme. The model simulation is also used to examine the potential for Arctic ozone destruction and the relative contributions of the chemical cycles responsible.

  9. Three-dimensional accurate detection of lung emphysema in rats using ultra-short and zero echo time MRI.

    PubMed

    Bianchi, Andrea; Tibiletti, Marta; Kjørstad, Åsmund; Birk, Gerald; Schad, Lothar R; Stierstorfer, Birgit; Rasche, Volker; Stiller, Detlef

    2015-11-01

    Emphysema is a life-threatening pathology that causes irreversible destruction of alveolar walls. In vivo imaging techniques play a fundamental role in the early non-invasive pre-clinical and clinical detection and longitudinal follow-up of this pathology. In the present study, we aimed to evaluate the feasibility of using high resolution radial three-dimensional (3D) zero echo time (ZTE) and 3D ultra-short echo time (UTE) MRI to accurately detect lung pathomorphological changes in a rodent model of emphysema.Porcine pancreas elastase (PPE) was intratracheally administered to the rats to produce the emphysematous changes. 3D ZTE MRI, low and high definition 3D UTE MRI and micro-computed tomography images were acquired 4 weeks after the PPE challenge. Signal-to-noise ratios (SNRs) were measured in PPE-treated and control rats. T2* values were computed from low definition 3D UTE MRI. Histomorphometric measurements were made after euthanizing the animals. Both ZTE and UTE MR images showed a significant decrease in the SNR measured in PPE-treated lungs compared with controls, due to the pathomorphological changes taking place in the challenged lungs. A significant decrease in T2* values in PPE-challenged animals compared with controls was measured using UTE MRI. Histomorphometric measurements showed a significant increase in the mean linear intercept in PPE-treated lungs. UTE yielded significantly higher SNR compared with ZTE (14% and 30% higher in PPE-treated and non-PPE-treated lungs, respectively).This study showed that optimized 3D radial UTE and ZTE MRI can provide lung images of excellent quality, with high isotropic spatial resolution (400 µm) and SNR in parenchymal tissue (>25) and negligible motion artifacts in freely breathing animals. These techniques were shown to be useful non-invasive instruments to accurately and reliably detect the pathomorphological alterations taking place in emphysematous lungs, without incurring the risks of cumulative radiation

  10. A solution accurate, efficient and stable unsplit staggered mesh scheme for three dimensional magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Lee, Dongwook

    2013-06-01

    In this paper, we extend the unsplit staggered mesh scheme (USM) for 2D magnetohydrodynamics (MHD) [D. Lee, A.E. Deane, An unsplit staggered mesh scheme for multidimensional magnetohydrodynamics, J. Comput. Phys. 228 (2009) 952-975] to a full 3D MHD scheme. The scheme is a finite-volume Godunov method consisting of a constrained transport (CT) method and an efficient and accurate single-step, directionally unsplit multidimensional data reconstruction-evolution algorithm, which extends Colella's original 2D corner transport upwind (CTU) method [P. Colella, Multidimensional upwind methods for hyperbolic conservation laws, J. Comput. Phys. 87 (1990) 446-466]. We present two types of data reconstruction-evolution algorithms for 3D: (1) a reduced CTU scheme and (2) a full CTU scheme. The reduced 3D CTU scheme is a variant of a simple 3D extension of Collela's 2D CTU method and is considered as a direct extension from the 2D USM scheme. The full 3D CTU scheme is our primary 3D solver which includes all multidimensional cross-derivative terms for stability. The latter method is logically analogous to the 3D unsplit CTU method by Saltzman [J. Saltzman, An unsplit 3D upwind method for hyperbolic conservation laws, J. Comput. Phys. 115 (1994) 153-168]. The major novelties in our algorithms are twofold. First, we extend the reduced CTU scheme to the full CTU scheme which is able to run with CFL numbers close to unity. Both methods utilize the transverse update technique developed in the 2D USM algorithm to account for transverse fluxes without solving intermediate Riemann problems, which in turn gives cost-effective 3D methods by reducing the total number of Riemann solves. The proposed algorithms are simple and efficient especially when including multidimensional MHD terms that maintain in-plane magnetic field dynamics. Second, we introduce a new CT scheme that makes use of proper upwind information in taking averages of electric fields. Our 3D USM schemes can be easily

  11. A three-dimensional characterization of coarse glacial outwash used for modeling contaminant movement

    SciTech Connect

    Aiken, J.S. ); Mickelson, D.M.; Anderson, M.P. . Dept. of Geology and Geophysics)

    1994-04-01

    Various mathematical and statistical techniques are employed to predict contaminant movement at multiple scales in heterogeneous aquifers. However, all of these methods require real geologic information to both design and calibrate models intended to predict contaminant movement accurately. A considerable gap exists between the ability of the hydrogeologist to construct models of heterogeneity and the availability of field data on which to base and compare these simulations. The gap exists because detailed geologic information is usually not available for a specific site without enormous expenditures of time and money. To bridge this gap, a field mapping project was undertaken to provide an example of outwash heterogeneity. The three-dimensional distribution of sediments was mapped in outcrop as it was incrementally exposed during commercial quarrying of a coarse out was deposit in south-central Wisconsin. Grain size sample measurements were used to estimate the hydrogeologic properties of the mapped units (facies). These data were combined to construct a three-dimensional map and a numerical model based on the distribution of the mapped heterogeneities. The model was then used to simulate groundwater flow and was linked to a particle tracking code to demonstrate the effect of the facies on contaminant movement.

  12. Predicting bite force in mammals: two-dimensional versus three-dimensional lever models.

    PubMed

    Davis, J L; Santana, S E; Dumont, E R; Grosse, I R

    2010-06-01

    Bite force is a measure of whole-organism performance that is often used to investigate the relationships between performance, morphology and fitness. When in vivo measurements of bite force are unavailable, researchers often turn to lever models to predict bite forces. This study demonstrates that bite force predictions based on two-dimensional (2-D) lever models can be improved by including three-dimensional (3-D) geometry and realistic physiological cross-sectional areas derived from dissections. Widely used, the 2-D method does a reasonable job of predicting bite force. However, it does so by over predicting physiological cross-sectional areas for the masseter and pterygoid muscles and under predicting physiological cross-sectional areas for the temporalis muscle. We found that lever models that include the three dimensional structure of the skull and mandible and physiological cross-sectional areas calculated from dissected muscles provide the best predictions of bite force. Models that accurately represent the biting mechanics strengthen our understanding of which variables are functionally relevant and how they are relevant to feeding performance. PMID:20472771

  13. Verification and Validation of a Three-Dimensional Generalized Composite Material Model

    NASA Technical Reports Server (NTRS)

    Hoffarth, Canio; Harrington, Joseph; Subramaniam, D. Rajan; Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Blankenhorn, Gunther

    2014-01-01

    A general purpose orthotropic elasto-plastic computational constitutive material model has been developed to improve predictions of the response of composites subjected to high velocity impact. The three-dimensional orthotropic elasto-plastic composite material model is being implemented initially for solid elements in LS-DYNA as MAT213. In order to accurately represent the response of a composite, experimental stress-strain curves are utilized as input, allowing for a more general material model that can be used on a variety of composite applications. The theoretical details are discussed in a companion paper. This paper documents the implementation, verification and qualitative validation of the material model using the T800- F3900 fiber/resin composite material.

  14. Verification and Validation of a Three-Dimensional Generalized Composite Material Model

    NASA Technical Reports Server (NTRS)

    Hoffarth, Canio; Harrington, Joseph; Rajan, Subramaniam D.; Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Blankenhorn, Gunther

    2015-01-01

    A general purpose orthotropic elasto-plastic computational constitutive material model has been developed to improve predictions of the response of composites subjected to high velocity impact. The three-dimensional orthotropic elasto-plastic composite material model is being implemented initially for solid elements in LS-DYNA as MAT213. In order to accurately represent the response of a composite, experimental stress-strain curves are utilized as input, allowing for a more general material model that can be used on a variety of composite applications. The theoretical details are discussed in a companion paper. This paper documents the implementation, verification and qualitative validation of the material model using the T800-F3900 fiber/resin composite material

  15. Assessing waveform predictions of recent three-dimensional velocity models of Tibet

    NASA Astrophysics Data System (ADS)

    Bao, X.; Shen, Y.

    2015-12-01

    High-resolution tomographic models are essential for understanding the physical and compositional properties in the lithosphere and obtaining accurate earthquake source locations and moment tensors. Yet, there are significant disagreements in recent three-dimensional velocity models of the crust and uppermost mantle in Tibet. Question also remains as to whether models constructed from one type of seismic waves (body or surface waves) can be used to predict travel times and waveforms of another. In this study, six global or regional models are selected for Tibet, most of which became publically available in the past five years. A three-dimensional finite-difference method in the spherical coordinates is applied to simulate full-wave propagation of regional Pn (with periods longer than 1 second) and Rayleigh waves (20-75 s period) for ground-truth events located at regional distances. The models are evaluated based on the phase delays and cross-correlation coefficients between synthetic and observed waveforms. A model generated from full-wave ambient noise tomography by Shen and Zhang (2012) consistently produces the best predictions for Rayleigh waves throughout the dataset and the Pn waves for the paths from the Tarim Basin to central Tibet. LITHO1.0, inverted from surface wave dispersions, shows a relatively stable but intermediate performance in predicting Pn and Rayleigh waves. None of the models provide the best matches to both waves throughout the region. Furthermore, the models constructed from surface waves are not well suited to predict Pn, and vice versa. We attribute this mainly to lack of accurate constraints on radial anisotropy and Vp/Vs ratios in the upper mantle, and Moho topography. We conclude that simultaneous prediction for P, S, and surface waves requires an integrated velocity model constructed with multiple seismic waveforms and consideration of other important properties, such as anisotropy and attenuation.

  16. Usefulness Of Three-Dimensional Printing Models for Patients with Stoma Construction

    PubMed Central

    Tominaga, Tetsuro; Takagi, Katsunori; Takeshita, Hiroaki; Miyamoto, Tomo; Shimoda, Kozue; Matsuo, Ayano; Matsumoto, Keitaro; Hidaka, Shigekazu; Yamasaki, Naoya; Sawai, Terumitsu; Nagayasu, Takeshi

    2016-01-01

    The use of patient-specific organ models in three-dimensional printing systems could be helpful for the education of patients and medical students. The aim of this study was to clarify whether the use of patient-specific stoma models is helpful for patient education. From January 2014 to September 2014, 5 patients who underwent colorectal surgery and for whom a temporary or permanent stoma had been created were involved in this study. Three-dimensional stoma models and three-dimensional face plates were created. The patients’ ages ranged from 59 to 81 years. Four patients underwent stoma construction because of rectal cancer, and 1 underwent stoma construction because of colon stenosis secondary to recurrent cancer. All patients were educated about their stoma and potential stoma-associated problems using three-dimensional stoma models, and all practiced cutting face plates using three-dimensional face plates. The models were also used during medical staff conferences to discuss current issues. All patients understood their problems and finally became self-reliant. The recent availability of three-dimensional printers has enabled the creation of many organ models, and full-scale stoma and face plate models are now available for patient education on cutting an appropriately individualized face plate. Thus, three-dimensional printers could enable fewer skin problems than are currently associated with daily stomal care. PMID:27403103

  17. Usefulness Of Three-Dimensional Printing Models for Patients with Stoma Construction.

    PubMed

    Tominaga, Tetsuro; Takagi, Katsunori; Takeshita, Hiroaki; Miyamoto, Tomo; Shimoda, Kozue; Matsuo, Ayano; Matsumoto, Keitaro; Hidaka, Shigekazu; Yamasaki, Naoya; Sawai, Terumitsu; Nagayasu, Takeshi

    2016-01-01

    The use of patient-specific organ models in three-dimensional printing systems could be helpful for the education of patients and medical students. The aim of this study was to clarify whether the use of patient-specific stoma models is helpful for patient education. From January 2014 to September 2014, 5 patients who underwent colorectal surgery and for whom a temporary or permanent stoma had been created were involved in this study. Three-dimensional stoma models and three-dimensional face plates were created. The patients' ages ranged from 59 to 81 years. Four patients underwent stoma construction because of rectal cancer, and 1 underwent stoma construction because of colon stenosis secondary to recurrent cancer. All patients were educated about their stoma and potential stoma-associated problems using three-dimensional stoma models, and all practiced cutting face plates using three-dimensional face plates. The models were also used during medical staff conferences to discuss current issues. All patients understood their problems and finally became self-reliant. The recent availability of three-dimensional printers has enabled the creation of many organ models, and full-scale stoma and face plate models are now available for patient education on cutting an appropriately individualized face plate. Thus, three-dimensional printers could enable fewer skin problems than are currently associated with daily stomal care. PMID:27403103

  18. A THREE-DIMENSIONAL MODEL ASSESSMENT OF THE GLOBAL DISTRIBUTION OF HEXACHLOROBENZENE

    EPA Science Inventory

    The distributions of persistent organic pollutants (POPs) in the global environment have been studied typically with box/fugacity models with simplified treatments of atmospheric transport processes1. Such models are incapable of simulating the complex three-dimensional mechanis...

  19. Reconstruction of heat flux profile on the HL-2A divertor plate with a three-dimensional analysis model

    NASA Astrophysics Data System (ADS)

    Gao, Jin-Ming; Li, Wei; Xia, Zhi-Wei; Pan, Yu-Dong; Lu, Jie; Yi, Ping; Liu, Yi

    2013-01-01

    A three-dimensional analysis model based on the finite element method (FEM) is developed, which can derive the evolution and distribution characteristics of heat flux deposited on the divertor plate from the surface temperature measured by infrared thermography diagnostics. The numerical simulations of surface heating due to localized power bursts and the power deposition calculations demonstrate that this analysis can provide accurate results and useful information about localized hot spots compared with the normal one- and two-dimensional calculations. In this paper, the details of this three-dimensional analysis are presented, and some results in ohmic heating and electron cyclotron resonant heating (ECRH) discharge on HL-2A are given.

  20. Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

    SciTech Connect

    Tourret, D.; Karma, A.; Clarke, A. J.; Gibbs, P. J.; Imhoff, S. D.

    2015-06-11

    We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulations and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.

  1. Three-dimensional Dendritic Needle Network model with application to Al-Cu directional solidification experiments

    DOE PAGES

    Tourret, D.; Karma, A.; Clarke, A. J.; Gibbs, P. J.; Imhoff, S. D.

    2015-06-11

    We present a three-dimensional (3D) extension of a previously proposed multi-scale Dendritic Needle Network (DNN) approach for the growth of complex dendritic microstructures. Using a new formulation of the DNN dynamics equations for dendritic paraboloid-branches of a given thickness, one can directly extend the DNN approach to 3D modeling. We validate this new formulation against known scaling laws and analytical solutions that describe the early transient and steady-state growth regimes, respectively. Finally, we compare the predictions of the model to in situ X-ray imaging of Al-Cu alloy solidification experiments. The comparison shows a very good quantitative agreement between 3D simulationsmore » and thin sample experiments. It also highlights the importance of full 3D modeling to accurately predict the primary dendrite arm spacing that is significantly over-estimated by 2D simulations.« less

  2. System for generating two-dimensional masks from a three-dimensional model using topological analysis

    DOEpatents

    Schiek, Richard

    2006-06-20

    A method of generating two-dimensional masks from a three-dimensional model comprises providing a three-dimensional model representing a micro-electro-mechanical structure for manufacture and a description of process mask requirements, reducing the three-dimensional model to a topological description of unique cross sections, and selecting candidate masks from the unique cross sections and the cross section topology. The method further can comprise reconciling the candidate masks based on the process mask requirements description to produce two-dimensional process masks.

  3. Innovations in hip arthroplasty three-dimensional modeling and analytical technology (SOMA).

    PubMed

    Banerjee, Samik; Faizan, Ahmad; Nevelos, Jim; Kreuzer, Stefan; Burgkart, Rainer; Harwin, Steven F; Mont, Michael A

    2014-03-01

    The modern generations of cementless hip arthroplasty implant designs are based on precise fit and fill of components within the native bony geometry of the proximal femur and the acetabulum for enhanced implant longevity. Variations exist based on a number of population demographics such as age, gender, body mass index, and ethnicity. Recently, establishment of comprehensive electronic computerized tomographic databases from a diverse population worldwide have been key innovations in the field of implant development. This technology provides a potential improvement compared to historical techniques of implant design and manufacturing which involved limited trials on cadavers. Segmentation of the computerized data to generate three-dimensional models allows precise and accurate measurements of anatomical structures and may provide better understanding of anthropometric variations that occur among individuals. Evidence-and population-based computational analyses may provide a better tool for designing orthopaedic implants that deliver an enhanced fit for a more diverse patient population. Moreover, these population-based databases can also verify new designs by means of virtual implantation and analysis on specific or large groups of bones within the database. The aim of this paper is to describe a three dimensional modeling and analytical technology and to review the various applications of this technology in relation to hip arthroplasty.

  4. New classification of lingual arch form in normal occlusion using three dimensional virtual models

    PubMed Central

    Park, Kyung Hee; Bayome, Mohamed; Park, Jae Hyun; Lee, Jeong Woo; Baek, Seung-Hak

    2015-01-01

    Objective The purposes of this study were 1) to classify lingual dental arch form types based on the lingual bracket points and 2) to provide a new lingual arch form template based on this classification for clinical application through the analysis of three-dimensional virtual models of normal occlusion sample. Methods Maxillary and mandibular casts of 115 young adults with normal occlusion were scanned in their occluded positions and lingual bracket points were digitized on the virtual models by using Rapidform 2006 software. Sixty-eight cases (dataset 1) were used in K-means cluster analysis to classify arch forms with intercanine, interpremolar and intermolar widths and width/depth ratios as determinants. The best-fit curves of the mean arch forms were generated. The remaining cases (dataset 2) were mapped into the obtained clusters and a multivariate test was performed to assess the differences between the clusters. Results Four-cluster classification demonstrated maximum intercluster distance. Wide, narrow, tapering, and ovoid types were described according to the intercanine and intermolar widths and their best-fit curves were depicted. No significant differences in arch depths existed among the clusters. Strong to moderate correlations were found between maxillary and mandibular arch widths. Conclusions Lingual arch forms have been classified into 4 types based on their anterior and posterior dimensions. A template of the 4 arch forms has been depicted. Three-dimensional analysis of the lingual bracket points provides more accurate identification of arch form and, consequently, archwire selection. PMID:25798413

  5. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models.

    PubMed

    Lawley, Sean D; Tuft, Marie; Brooks, Heather A

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  6. A system for quantitative morphological measurement and electronic modelling of neurons: three-dimensional reconstruction.

    PubMed

    Stockley, E W; Cole, H M; Brown, A D; Wheal, H V

    1993-04-01

    A system for accurately reconstructing neurones from optical sections taken at high magnification is described. Cells are digitised on a 68000-based microcomputer to form a database consisting of a series of linked nodes each consisting of x, y, z coordinates and an estimate of dendritic diameter. This database is used to generate three-dimensional (3-D) displays of the neurone and allows quantitative analysis of the cell volume, surface area and dendritic length. Images of the cell can be manipulated locally or transferred to an IBM 3090 mainframe where a wireframe model can be displayed on an IBM 5080 graphics terminal and rotated interactively in real time, allowing visualisation of the cell from all angles. Space-filling models can also be produced. Reconstructions can also provide morphological data for passive electrical simulations of hippocampal pyramidal cells.

  7. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

    NASA Astrophysics Data System (ADS)

    Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  8. Three-Dimensional Electro-Thermal Verilog-A Model of Power MOSFET for Circuit Simulation

    NASA Astrophysics Data System (ADS)

    Chvála, A.; Donoval, D.; Marek, J.; Príbytný, P.; Molnár, M.; Mikolášek, M.

    2014-04-01

    New original circuit model for the power device based on interactive coupling of electrical and thermal properties is described. The thermal equivalent network for a three-dimensional heat flow is presented. Designed electro-thermal MOSFET model for circuit simulations with distributed properties and three-dimensional thermal equivalent network is used for simulation of multipulse unclamped inductive switching (UIS) test of device robustness. The features and the limitations of the new model are analyzed and presented.

  9. Survey of three-dimensional numerical estuarine models

    USGS Publications Warehouse

    Cheng, Ralph T.; Smith, Peter E.

    1989-01-01

    This paper surveys the existing 3-D estuarine hydrodynamic and solute transport models by a review of the commonly used assumptions and approximations, and by an examination of the methods of solution. The model formulations, methods of solution, and known applications are surveyed and summarized in tables. In conclusion, the authors present their modeling philosophy and suggest future research needs.

  10. Assessing waveform predictions of recent three-dimensional velocity models of the Tibetan Plateau

    NASA Astrophysics Data System (ADS)

    Bao, Xueyang; Shen, Yang

    2016-04-01

    Accurate velocity models are essential for both the determination of earthquake locations and source moments and the interpretation of Earth structures. With the increasing number of three-dimensional velocity models, it has become necessary to assess the models for accuracy in predicting seismic observations. Six models of the crustal and uppermost mantle structures in Tibet and surrounding regions are investigated in this study. Regional Rayleigh and Pn (or Pnl) waveforms from two ground truth events, including one nuclear explosion and one natural earthquake located in the study area, are simulated by using a three-dimensional finite-difference method. Synthetics are compared to observed waveforms in multiple period bands of 20-75 s for Rayleigh waves and 1-20 s for Pn/Pnl waves. The models are evaluated based on the phase delays and cross-correlation coefficients between synthetic and observed waveforms. A model generated from full-wave ambient noise tomography best predicts Rayleigh waves throughout the data set, as well as Pn/Pnl waves traveling from the Tarim Basin to the stations located in central Tibet. In general, the models constructed from P wave tomography are not well suited to predict Rayleigh waves, and vice versa. Possible causes of the differences between observed and synthetic waveforms, and frequency-dependent variations of the "best matching" models with the smallest prediction errors are discussed. This study suggests that simultaneous prediction for body and surface waves requires an integrated velocity model constructed with multiple seismic waveforms and consideration of other important properties, such as anisotropy.

  11. Three-dimensional models of non-NMDA glutamate receptors.

    PubMed Central

    Sutcliffe, M J; Wo, Z G; Oswald, R E

    1996-01-01

    Structural models have been produced for three types of non-NMDA inotropic glutamate receptors: an AMPA receptor, GluR1, a kainate receptor, GluR6; and a low-molecular-weight kainate receptor from goldfish, GFKAR alpha. Modeling was restricted to the domains of the proteins that bind the neurotransmitter glutamate and that form the ion channel. Model building combined homology modeling, distance geometry, molecular mechanics, interactive modeling, and known constraints. The models indicate new potential interactions in the extracellular domain between protein and agonists, and suggest that the transition from the "closed" to the "open" state involves the movement of a conserved positive residue away from, and two conserved negative residues into, the extracellular entrance to the pore upon binding. As a first approximation, the ion channel domain was modeled with a structure comprising a central antiparallel beta-barrel that partially crosses the membrane, and against which alpha-helices from each subunit are packed; a third alpha-helix packs against these two helices in each subunit. Much, but not all, of the available data were consistent with this structure. Modifying the beta-barrel to a loop-like topology produced a model consistent with available data. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 7 PMID:8785317

  12. Three-Dimensional Ultrasound-Derived Physical Mitral Valve Modeling

    PubMed Central

    Witschey, Walter RT; Pouch, Alison M; McGarvey, Jeremy R; Ikeuchi, Kaori; Contijoch, Francisco; Levack, Melissa M; Yushkevick, Paul A; Sehgal, Chandra M; Jackson, Benjamin; Gorman, Robert C; Gorman, Joseph H

    2015-01-01

    Purpose Advances in mitral valve repair and adoption have been partly attributed to improvements in echocardiographic imaging technology. To further educate and guide repair surgery, we have developed a methodology to quickly produce physical models of the valve using novel 3D echocardiographic imaging software in combination with stereolithographic printing. Description Quantitative virtual mitral valve shape models were developed from 3D transesophageal echocardiographic images using software based on semi-automated image segmentation and continuous medial representation (cm-rep) algorithms. These quantitative virtual shape models were then used as input to a commercially available stereolithographic printer to generate a physical model of the each valve at end systole and end diastole. Evaluation Physical models of normal and diseased valves (ischemic mitral regurgitation and myxomatous degeneration) were constructed. There was good correspondence between the virtual shape models and physical models. Conclusions It was feasible to create a physical model of mitral valve geometry under normal, ischemic and myxomatous valve conditions using 3D printing of 3D echocardiographic data. Printed valves have the potential to guide surgical therapy for mitral valve disease. PMID:25087790

  13. Crisis Assessment: A Three-Dimensional Model for Triage.

    ERIC Educational Resources Information Center

    Myer, Rick A.; And Others

    1992-01-01

    Presents triage assessment model for crisis intervention that enables mental health counselors to initiate appropriate crisis interventions in variety of situations. Model guides assessment of clients in crisis on three domains: affective, cognitive, and behavioral. Describes assessment and rating of severity of impairment for each of the three…

  14. Three Dimensional Thermal Model of Newberry Volcano, Oregon

    DOE Data Explorer

    Trenton Cladouhos

    2015-01-30

    Final results of a 3D finite difference thermal model of Newberry Volcano, Oregon. Model data are formatted as a text file with four data columns (X, Y, Z, T). X and Y coordinates are in UTM (NAD83 Zone 10N), Z is elevation from mean sea level (meters), T is temperature in °C. Model is 40km X 40km X 12.5 km, grid node spacing is 100m in X, Y, and Z directions. A symmetric cylinder shaped magmatic heat source centered on the present day caldera is the modeled heat source. The center of the modeled body is a -1700 m (elevation) and is 600m thick with a radius of 8700m. This is the best fit results from 2D modeling of the west flank of the volcano. The model accounts for temperature dependent thermal properties and latent heat of crystallization. For additional details, assumptions made, data used, and a discussion of the validity of the model see Frone, 2015 (http://search.proquest.com/docview/1717633771).

  15. Three-dimensional developing flow model for photocatalytic monolith reactors

    SciTech Connect

    Hossain, Md.M.; Raupp, G.B.; Hay, S.O.; Obee, T.N.

    1999-06-01

    A first-principles mathematical model describes performance of a titania-coated honeycomb monolith photocatalytic oxidation (PCO) reactor for air purification. The single-channel, 3-D convection-diffusion-reaction model assumes steady-state operation, negligible axial dispersion, and negligible homogeneous reaction. The reactor model accounts rigorously for entrance effects arising from the developing fluid-flow field and uses a previously developed first-principles radiation-field submodel for the UV flux profile down the monolith length. The model requires specification of an intrinsic photocatalytic reaction rate dependent on local UV light intensity and local reactant concentration, and uses reaction-rate expressions and kinetic parameters determined independently using a flat-plate reactor. Model predictions matched experimental pilot-scale formaldehyde conversion measurements for a range of inlet formaldehyde concentrations, air humidity levels, monolith lengths, and for various monolith/lamp-bank configurations. This agreement was realized without benefit of any adjustable photocatalytic reactor model parameters, radiation-field submodel parameters, or kinetic submodel parameters. The model tends to systematically overpredict toluene conversion data by about 33%, which falls within the accepted limits of experimental kinetic parameter accuracy. With further validation, the model could be used in PCO reactor design and to develop quantitative energy utilization metrics.

  16. Development of a Three-Dimensional Hand Model Using Three-Dimensional Stereophotogrammetry: Assessment of Image Reproducibility

    PubMed Central

    Hoevenaren, Inge A.; Meulstee, J.; Krikken, E.; Bergé, S. J.; Ulrich, D. J. O.; Maal, Thomas J. J.

    2015-01-01

    Purpose Using three-dimensional (3D) stereophotogrammetry precise images and reconstructions of the human body can be produced. Over the last few years, this technique is mainly being developed in the field of maxillofacial reconstructive surgery, creating fusion images with computed tomography (CT) data for precise planning and prediction of treatment outcome. Though, in hand surgery 3D stereophotogrammetry is not yet being used in clinical settings. Methods A total of 34 three-dimensional hand photographs were analyzed to investigate the reproducibility. For every individual, 3D photographs were captured at two different time points (baseline T0 and one week later T1). Using two different registration methods, the reproducibility of the methods was analyzed. Furthermore, the differences between 3D photos of men and women were compared in a distance map as a first clinical pilot testing our registration method. Results The absolute mean registration error for the complete hand was 1.46 mm. This reduced to an error of 0.56 mm isolating the region to the palm of the hand. When comparing hands of both sexes, it was seen that the male hand was larger (broader base and longer fingers) than the female hand. Conclusions This study shows that 3D stereophotogrammetry can produce reproducible images of the hand without harmful side effects for the patient, so proving to be a reliable method for soft tissue analysis. Its potential use in everyday practice of hand surgery needs to be further explored. PMID:26366860

  17. Flow Induced Vibration and Glottal Aerodynamics in a Three-Dimensional Laryngeal Model

    NASA Astrophysics Data System (ADS)

    Zheng, Xudong; Xue, Qian; Mittal, Rajat; Bielamowicz, Steven

    2009-11-01

    Three-dimensional effects associated with phonation remain unclear due to the lack of capability of simulating 3D fluid-tissue interaction in the past. To advance the state-of-the-art in this arena, an immersed-boundary method based flow solver coupled with a finite-element solid dynamics solver is employed to conduct high-fidelity direct-numerical simulations of phonation in a 3D model of the human larynx. Three-dimensional vibration patterns are captured along with turbulence effects and three-dimensional vortex structures in the glottal jet. Results from these simulations are presented.

  18. Observation-driven adaptive differential evolution and its application to accurate and smooth bronchoscope three-dimensional motion tracking.

    PubMed

    Luo, Xiongbiao; Wan, Ying; He, Xiangjian; Mori, Kensaku

    2015-08-01

    This paper proposes an observation-driven adaptive differential evolution algorithm that fuses bronchoscopic video sequences, electromagnetic sensor measurements, and computed tomography images for accurate and smooth bronchoscope three-dimensional motion tracking. Currently an electromagnetic tracker with a position sensor fixed at the bronchoscope tip is commonly used to estimate bronchoscope movements. The large tracking error from directly using sensor measurements, which may be deteriorated heavily by patient respiratory motion and the magnetic field distortion of the tracker, limits clinical applications. How to effectively use sensor measurements for precise and stable bronchoscope electromagnetic tracking remains challenging. We here exploit an observation-driven adaptive differential evolution framework to address such a challenge and boost the tracking accuracy and smoothness. In our framework, two advantageous points are distinguished from other adaptive differential evolution methods: (1) the current observation including sensor measurements and bronchoscopic video images is used in the mutation equation and the fitness computation, respectively and (2) the mutation factor and the crossover rate are determined adaptively on the basis of the current image observation. The experimental results demonstrate that our framework provides much more accurate and smooth bronchoscope tracking than the state-of-the-art methods. Our approach reduces the tracking error from 3.96 to 2.89 mm, improves the tracking smoothness from 4.08 to 1.62 mm, and increases the visual quality from 0.707 to 0.741. PMID:25660001

  19. Three-dimensional effects for radio frequency antenna modeling

    NASA Astrophysics Data System (ADS)

    Carter, M. D.; Batchelor, D. B.; Stallings, D. C.

    1993-09-01

    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. Comparisons with experiments indicate that these 2-D calculations can overestimate the loading of the antenna and fail to give the correct reactive behavior. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform 3-D modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused by feeders to the main current strap, conducting sidewalls, and finite phase velocity are considered. The plasma impedance matrix for the loading calculation is generated by use of the ORION-1D code. The 3-D model is benchmarked with the 2-D model in the 2-D limit. For finite-length antennas, inductance calculations are found to be in much more reasonable agreement with experiments for 3-D modeling than for the 2-D estimates. 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 sidewalls rather than in the plasma as in the 2-D model. Thus, the feeders have much more influence than the plasma on the currents that return in the sidewall. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading 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.

  20. Three-dimensional effects for radio frequency antenna modeling

    SciTech Connect

    Carter, M.D.; Batchelor, D.B.; Stallings, D.C.

    1993-09-01

    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. Comparisons with experiments indicate that these 2-D calculations can overestimate the loading of the antenna and fail to give the correct reactive behavior. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform 3-D modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused by feeders to the main current strap, conducting sidewalls, and finite phase velocity are considered. The plasma impedance matrix for the loading calculation is generated by use of the ORION-1D code. The 3-D model is benchmarked with the 2-D model in the 2-D limit. For finite-length antennas, inductance calculations are found to be in much more reasonable agreement with experiments for 3-D modeling than for the 2-D estimates. 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 sidewalls rather than in the plasma as in the 2-D model. Thus, the feeders have much more influence than the plasma on the currents that return in the sidewall. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading 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.

  1. Three-dimensional statistical model for gingival contour reconstruction.

    PubMed

    Wu, Ting; Liao, Wenhe; Dai, Ning

    2012-04-01

    Optimal gingival contours around restored teeth and implants are of critical importance for restorative success and esthetics. This paper describes a novel computer-aided methodology for building a 3-D statistical model of gingival contours from a 3-D scan dental dataset and reconstructing missing gingival contours in partially edentulous patients. The gingival boundaries were first obtained from the 3-D dental model through a discrete curvature analysis and shortest path searching algorithm. Based on the gingival shape differential characteristics, the boundaries were demarcated to construct the gingival contour of each individual tooth. Through B-spline curve approximation to each gingival contour, the control points of the B-spline curves are used as the shape vector for training the model. Statistical analysis results demonstrate that the method can give a simple but compact model that effectively capture the most important variations in arch width and shape as well as gingival morphology and position. Within this statistical model, the morphologically plausible missing contours can be inferred based on a nonlinear optimization fitting from the global similarity transformation, the model shape deformation and a Mahalanobis prior. The reconstruction performance is evaluated through large simulated experimental data and a real patient case, which demonstrates the effectiveness of this approach.

  2. A recapitulative three-dimensional model of breast carcinoma requires perfusion for multi-week growth.

    PubMed

    Goliwas, Kayla F; Marshall, Lauren E; Ransaw, Evette L; Berry, Joel L; Frost, Andra R

    2016-01-01

    Breast carcinomas are complex, three-dimensional tissues composed of cancer epithelial cells and stromal components, including fibroblasts and extracellular matrix. In vitro models that more faithfully recapitulate this dimensionality and stromal microenvironment should more accurately elucidate the processes driving carcinogenesis, tumor progression, and therapeutic response. Herein, novel in vitro breast carcinoma surrogates, distinguished by a relevant dimensionality and stromal microenvironment, are described and characterized. A perfusion bioreactor system was used to deliver medium to surrogates containing engineered microchannels and the effects of perfusion, medium composition, and the method of cell incorporation and density of initial cell seeding on the growth and morphology of surrogates were assessed. Perfused surrogates demonstrated significantly greater cell density and proliferation and were more histologically recapitulative of human breast carcinoma than surrogates maintained without perfusion. Although other parameters of the surrogate system, such as medium composition and cell seeding density, affected cell growth, perfusion was the most influential parameter. PMID:27516850

  3. Three-dimensional modeling of beam emission spectroscopy measurements in fusion plasmas

    SciTech Connect

    Guszejnov, D.; Pokol, G. I.; Pusztai, I.; Refy, D.; Zoletnik, S.; Lampert, M.; Nam, Y. U.

    2012-11-15

    One of the main diagnostic tools for measuring electron density profiles and the characteristics of long wavelength turbulent wave structures in fusion plasmas is beam emission spectroscopy (BES). The increasing number of BES systems necessitated an accurate and comprehensive simulation of BES diagnostics, which in turn motivated the development of the Rate Equations for Neutral Alkali-beam TEchnique (RENATE) simulation code that is the topic of this paper. RENATE is a modular, fully three-dimensional code incorporating all key features of BES systems from the atomic physics to the observation, including an advanced modeling of the optics. Thus RENATE can be used both in the interpretation of measured signals and the development of new BES systems. The most important components of the code have been successfully benchmarked against other simulation codes. The primary results have been validated against experimental data from the KSTAR tokamak.

  4. Three-dimensional modeling of a patent ductus arteriosus in a cat.

    PubMed

    Saunders, A B; Birch, S A

    2015-12-01

    A left-to-right shunting patent ductus arteriosus was diagnosed in a 13-week-old, 2.5 kg, male, domestic Shorthair cat with a continuous murmur. Echocardiographic abnormalities were identified, including: cardiomegaly, wide and presumably short ductal ampulla, and a large right branch pulmonary artery. When these findings were combined with the small patient size, additional imaging was considered prior to surgical ligation, and computed tomography angiography was preferred over standard angiography to provide multi-dimensional appreciation of the anatomy prior to surgery. The dataset from a computed tomography angiographic study performed prior to surgical ligation was used to create a three-dimensional model of the heart and great vessels. The rendered images accurately depicted the cardiac anatomy in situ, which can be utilized for surgical procedural planning and to enhance visuospatial understanding of the anatomy at all levels of training. PMID:26776592

  5. Three-dimensional modeling of beam emission spectroscopy measurements in fusion plasmas

    NASA Astrophysics Data System (ADS)

    Guszejnov, D.; Pokol, G. I.; Pusztai, I.; Refy, D.; Zoletnik, S.; Lampert, M.; Nam, Y. U.

    2012-11-01

    One of the main diagnostic tools for measuring electron density profiles and the characteristics of long wavelength turbulent wave structures in fusion plasmas is beam emission spectroscopy (BES). The increasing number of BES systems necessitated an accurate and comprehensive simulation of BES diagnostics, which in turn motivated the development of the Rate Equations for Neutral Alkali-beam TEchnique (RENATE) simulation code that is the topic of this paper. RENATE is a modular, fully three-dimensional code incorporating all key features of BES systems from the atomic physics to the observation, including an advanced modeling of the optics. Thus RENATE can be used both in the interpretation of measured signals and the development of new BES systems. The most important components of the code have been successfully benchmarked against other simulation codes. The primary results have been validated against experimental data from the KSTAR tokamak.

  6. Three-dimensional modeling of beam emission spectroscopy measurements in fusion plasmas.

    PubMed

    Guszejnov, D; Pokol, G I; Pusztai, I; Refy, D; Zoletnik, S; Lampert, M; Nam, Y U

    2012-11-01

    One of the main diagnostic tools for measuring electron density profiles and the characteristics of long wavelength turbulent wave structures in fusion plasmas is beam emission spectroscopy (BES). The increasing number of BES systems necessitated an accurate and comprehensive simulation of BES diagnostics, which in turn motivated the development of the Rate Equations for Neutral Alkali-beam TEchnique (RENATE) simulation code that is the topic of this paper. RENATE is a modular, fully three-dimensional code incorporating all key features of BES systems from the atomic physics to the observation, including an advanced modeling of the optics. Thus RENATE can be used both in the interpretation of measured signals and the development of new BES systems. The most important components of the code have been successfully benchmarked against other simulation codes. The primary results have been validated against experimental data from the KSTAR tokamak.

  7. A recapitulative three-dimensional model of breast carcinoma requires perfusion for multi-week growth

    PubMed Central

    Goliwas, Kayla F; Marshall, Lauren E; Ransaw, Evette L; Berry, Joel L; Frost, Andra R

    2016-01-01

    Breast carcinomas are complex, three-dimensional tissues composed of cancer epithelial cells and stromal components, including fibroblasts and extracellular matrix. In vitro models that more faithfully recapitulate this dimensionality and stromal microenvironment should more accurately elucidate the processes driving carcinogenesis, tumor progression, and therapeutic response. Herein, novel in vitro breast carcinoma surrogates, distinguished by a relevant dimensionality and stromal microenvironment, are described and characterized. A perfusion bioreactor system was used to deliver medium to surrogates containing engineered microchannels and the effects of perfusion, medium composition, and the method of cell incorporation and density of initial cell seeding on the growth and morphology of surrogates were assessed. Perfused surrogates demonstrated significantly greater cell density and proliferation and were more histologically recapitulative of human breast carcinoma than surrogates maintained without perfusion. Although other parameters of the surrogate system, such as medium composition and cell seeding density, affected cell growth, perfusion was the most influential parameter. PMID:27516850

  8. Preliminary results of a three-dimensional radiative transfer model

    SciTech Connect

    O`Hirok, W.

    1995-09-01

    Clouds act as the primary modulator of the Earth`s radiation at the top of the atmosphere, within the atmospheric column, and at the Earth`s surface. They interact with both shortwave and longwave radiation, but it is primarily in the case of shortwave where most of the uncertainty lies because of the difficulties in treating scattered solar radiation. To understand cloud-radiative interactions, radiative transfer models portray clouds as plane-parallel homogeneous entities to ease the computational physics. Unfortunately, clouds are far from being homogeneous, and large differences between measurement and theory point to a stronger need to understand and model cloud macrophysical properties. In an attempt to better comprehend the role of cloud morphology on the 3-dimensional radiation field, a Monte Carlo model has been developed. This model can simulate broadband shortwave radiation fluxes while incorporating all of the major atmospheric constituents. The model is used to investigate the cloud absorption anomaly where cloud absorption measurements exceed theoretical estimates and to examine the efficacy of ERBE measurements and cloud field experiments. 3 figs.

  9. Three-Dimensional Paper-Based Model for Cardiac Ischemia

    PubMed Central

    Mosadegh, Bobak; Dabiri, Borna E.; Lockett, Matthew R.; Derda, Ratmir; Campbell, Patrick; Parker, Kevin Kit; Whitesides, George M.

    2014-01-01

    In vitro models of ischemia have not historically recapitulated the cellular interactions and gradients of molecules that occur in a 3D tissue. This work demonstrates a paper-based 3D culture system that mimics some of the interactions that occur among populations of cells in the heart during ischemia. Multiple layers of paper containing cells, suspended in hydrogels, are stacked to form a layered 3D model of a tissue. Mass transport of oxygen and glucose into this 3D system can be modulated to induce an ischemic environment in the bottom layers of the stack. This ischemic stress induces cardiomyocytes at the bottom of the stack to secrete chemokines that subsequently trigger fibroblasts residing in adjacent layers to migrate toward the ischemic region. This work demonstrates the usefulness of patterned, stacked paper for performing in vitro mechanistic studies of cellular motility and viability within a model of the laminar ventricle tissue of the heart. PMID:24574054

  10. Reversible fragile watermarking scheme for three-dimensional models

    NASA Astrophysics Data System (ADS)

    Wang, Jen-Tse; Wang, Peng-Cheng; Yu, Shyr-Shen

    2009-09-01

    Watermarking is a very important technique for protecting the authorization of digital content, such as still images, video streams, audio streams, and 3-D models. Most fragile watermarking schemes for 3-D models are not reversible. Published reversible or irreversible fragile watermarking schemes for 3-D models have many drawbacks, such as the causality problem, not being blind, or being unable to locate changed regions. To overcome these drawbacks, a reversible fragile watermarking scheme for 3-D models in spatial domain is proposed. Principal component analysis (PCA) is employed to produce the PCA coordinate system and make the system robust against similarity transformation attacks. PCA, together with a novel interval embedding technique, provide the blind reversibility of the proposed scheme. Intervals larger than a threshold and smaller than another threshold are adopted as legitimate to avoid large distortion. Moreover, experimental results show that the proposed scheme can overcome the causality, convergence, and confusion problems; provide both tampering detection and better embedding rate and requiring a small key size.

  11. Parallelisation study of a three-dimensional environmental flow model

    NASA Astrophysics Data System (ADS)

    O'Donncha, Fearghal; Ragnoli, Emanuele; Suits, Frank

    2014-03-01

    There are many simulation codes in the geosciences that are serial and cannot take advantage of the parallel computational resources commonly available today. One model important for our work in coastal ocean current modelling is EFDC, a Fortran 77 code configured for optimal deployment on vector computers. In order to take advantage of our cache-based, blade computing system we restructured EFDC from serial to parallel, thereby allowing us to run existing models more quickly, and to simulate larger and more detailed models that were previously impractical. Since the source code for EFDC is extensive and involves detailed computation, it is important to do such a port in a manner that limits changes to the files, while achieving the desired speedup. We describe a parallelisation strategy involving surgical changes to the source files to minimise error-prone alteration of the underlying computations, while allowing load-balanced domain decomposition for efficient execution on a commodity cluster. The use of conjugate gradient posed particular challenges due to implicit non-local communication posing a hindrance to standard domain partitioning schemes; a number of techniques are discussed to address this in a feasible, computationally efficient manner. The parallel implementation demonstrates good scalability in combination with a novel domain partitioning scheme that specifically handles mixed water/land regions commonly found in coastal simulations. The approach presented here represents a practical methodology to rejuvenate legacy code on a commodity blade cluster with reasonable effort; our solution has direct application to other similar codes in the geosciences.

  12. Three-Dimensional Models for Teaching Neuroanatomy to Blind Students.

    ERIC Educational Resources Information Center

    Pietsch, Paul

    1980-01-01

    An audio/tactile course enables blind college students to understand the anatomy of the human brain. Models were designed which allow tactile exploration of the visual fields, retina, optic nerves, and the subdivisions of the tracts and radiations in the brain. (Author/PHR)

  13. Three-dimensional modelling and geothermal process simulation

    SciTech Connect

    Burns, K.L.

    1990-01-01

    The subsurface geological model or 3-D GIS is constructed from three kinds of objects, which are a lithotope (in boundary representation), a number of fault systems, and volumetric textures (vector fields). The chief task of the model is to yield an estimate of the conductance tensors (fluid permeability and thermal conductivity) throughout an array of voxels. This is input as material properties to a FEHM numerical physical process model. The main task of the FEHM process model is to distinguish regions of convective from regions of conductive heat flow, and to estimate the fluid phase, pressure and flow paths. The temperature, geochemical, and seismic data provide the physical constraints on the process. The conductance tensors in the Franciscan Complex are to be derived by the addition of two components. The isotropic component is a stochastic spatial variable due to disruption of lithologies in melange. The deviatoric component is deterministic, due to smoothness and continuity in the textural vector fields. This decomposition probably also applies to the engineering hydrogeological properties of shallow terrestrial fluvial systems. However there are differences in quantity. The isotropic component is much more variable in the Franciscan, to the point where volumetric averages are misleading, and it may be necessary to select that component from several, discrete possible states. The deviatoric component is interpolated using a textural vector field. The Franciscan field is much more complicated, and contains internal singularities. 27 refs., 10 figs.

  14. Three Dimensional Morphodynamic and Vegetation Modeling of Wax Lake Delta

    NASA Astrophysics Data System (ADS)

    Khadka, A. K.; Meselhe, E. A.; Sadid, K. M.

    2013-12-01

    The Wax Lake Delta (WLD) is located at the downstream end of the Wax Lake outlet, approximately 13 miles upstream from Morgan City, Louisiana. In 1942 the United States Army Corps of Engineer (USACE) dredged Wax Lake Outlet channel from lower Atchafalaya River to reduce flood stages at Morgan City. The channel diverts 50% of Atchafalaya River water and sediment to WLD. Since 1942, the WLD has been building seaward due to the deposition of sediment at the channel mouth. Growth of this delta supports the concept of land building via river diversions. A process based morphodynamic model (Delft3D) with the ability to predict evolution of river-dominated deltas is used in this study to further our understanding of land-building and delta growth processes. Initial model bathymetry is prepared based on USACE hydrographic survey of 1998 along with LIDAR survey data for over bank areas. Two continuous gauges at Wax Lake outlet near Calumet and Atchafalaya Bay near Eugene Island are used to assign upstream inflow and outflow boundary conditions, respectively. The model is calibrated and validated for Hydrodynamics and Sediment transport through two sets of field observations for flooded and average conditions. Vertical velocity and suspended sediment profiles made in the channels of the WLD in 2000 and 2001 are used for the model calibration and validation. More comprehensive field observations are being gathered as part of an ongoing study funded by the National Science Foundation (FESD-Delta Dynamics Collaboratory). Data include mutli-beam bathymetric data, velocities, sediment, and nutrient concentrations in the channels as well as on top of the islands. The Delft3D morphodynamic model for WLD provides quantitative information regarding water and sediment distribution among the inter-connected channel bifurcations, the exchange of sediment and nutrients between the channels and islands. The model is being used to investigate the rate of land building and delta growth from

  15. A three-dimensional model simulation of atmospheric nitrous oxide

    NASA Technical Reports Server (NTRS)

    Turner, R. E.; Blackshear, W. T.; Grose, W. L.; Eckman, R. S.; Pierce, R. B.; Fairlie, T. D. A.

    1992-01-01

    The NASA Langley 3D GCM chemical transport model is used to investigate the distribution of atmospheric N2O up to 60 km altitude. The transport characteristics of the model is evaluated without the complications of a detailed chemical formulation for all of the relevant stratospheric minor constituents. Interpretation of the yearly average zonal mean N2O distribution in terms of transport by the yearly averaged meridional circulation and stratospheric photochemical loss indicates large regions in the Northern Hemisphere stratosphere where dynamical mixing apparently plays a large role in maintaining the N2O distribution. In these regions, slopes of the N2O mixing ratio isopleths are maintained by competition between advection by the meridional circulation acting to steepen and dynamical mixing acting to flatten the slopes.

  16. Three-dimensional model of surfactant replacement therapy.

    PubMed

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

    2015-07-28

    Surfactant replacement therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. It is widely successful for treating surfactant deficiency in premature neonates who develop neonatal respiratory distress syndrome (NRDS). However, when applied to adults with acute respiratory distress syndrome (ARDS), early successes were followed by failures. This unexpected and puzzling situation is a vexing issue in the pulmonary community. A pressing question is whether the instilled surfactant mixture actually reaches the adult alveoli/acinus in therapeutic amounts. In this study, to our knowledge, we present the first mathematical model of SRT in a 3D lung structure to provide insight into answering this and other questions. The delivery is computed from fluid mechanical principals for 3D models of the lung airway tree for neonates and adults. A liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug deposits a coating film on the airway wall and then splits unevenly at the bifurcation due to gravity. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published procedural methods, we show the neonatal lung is a well-mixed compartment, whereas the adult lung is not. The earlier, successful adult SRT studies show comparatively good index values implying adequate delivery. The later, failed studies used different protocols resulting in very low values of both indexes, consistent with inadequate acinar delivery. Reasons for these differences and the evolution of failure from success are outlined and potential remedies discussed.

  17. Three-dimensional generalized xy models: A Monte Carlo study

    NASA Astrophysics Data System (ADS)

    Chamati, H.; Romano, S.; Mól, L. A. S.; Pereira, A. R.

    2005-10-01

    The lattice spin models considered in the present paper consist of three-component unit vectors, associated with a D-dimensional lattice (say Bbb Zd), parameterized by usual spherical angles (θk,phik), and interacting via a ferromagnetic potential restricted to nearest neighbours, of the form Wjk = - epsilon(sin θj sin θk)p cos (phij - phik), p in Bbb N, p >= 1; here epsilon is a positive quantity setting energy and temperature scales. The models were recently introduced, and rigorous comparison inequalities holding for them were investigated, and used to prove the existence of an ordering transition when D = 3 (Romano S. and Zagrebnov V. A., Phys. Lett. A, 301 (2002) 402), investigated by other approximate techniques as well (Mól L. A. S., Pereira A. R. and Moura-Melo W. A., Phys. Lett. A, 319 (2003) 114). We report here an extensive Monte Carlo study of the critical behaviour for D = 3 and p <= 4; our results are consistent with the same universality class as the xy model.

  18. A multiphase model for three-dimensional tumor growth

    PubMed Central

    Sciumè, G; Shelton, S; Gray, WG; Miller, CT; Hussain, F; Ferrari, M; Decuzzi, P; Schrefler, BA

    2014-01-01

    Several mathematical formulations have analyzed the time-dependent behaviour of a tumor mass. However, most of these propose simplifications that compromise the physical soundness of the model. Here, multiphase porous media mechanics is extended to model tumor evolution, using governing equations obtained via the Thermodynamically Constrained Averaging Theory (TCAT). A tumor mass is treated as a multiphase medium composed of an extracellular matrix (ECM); tumor cells (TC), which may become necrotic depending on the nutrient concentration and tumor phase pressure; healthy cells (HC); and an interstitial fluid (IF) for the transport of nutrients. The equations are solved by a Finite Element method to predict the growth rate of the tumor mass as a function of the initial tumor-to-healthy cell density ratio, nutrient concentration, mechanical strain, cell adhesion and geometry. Results are shown for three cases of practical biological interest such as multicellular tumor spheroids (MTS) and tumor cords. First, the model is validated by experimental data for time-dependent growth of an MTS in a culture medium. The tumor growth pattern follows a biphasic behaviour: initially, the rapidly growing tumor cells tend to saturate the volume available without any significant increase in overall tumor size; then, a classical Gompertzian pattern is observed for the MTS radius variation with time. A core with necrotic cells appears for tumor sizes larger than 150 μm, surrounded by a shell of viable tumor cells whose thickness stays almost constant with time. A formula to estimate the size of the necrotic core is proposed. In the second case, the MTS is confined within a healthy tissue. The growth rate is reduced, as compared to the first case – mostly due to the relative adhesion of the tumor and healthy cells to the ECM, and the less favourable transport of nutrients. In particular, for tumor cells adhering less avidly to the ECM, the healthy tissue is progressively displaced

  19. n-vicinities method for three dimensional Ising Model

    NASA Astrophysics Data System (ADS)

    Kryzhanovsky, Boris; Litinskii, Leonid

    2016-08-01

    The n -vicinities method for approximate calculations of the partition function of a spin system was proposed previously. The equation of state was obtained in the most general form. In the present publication these results are adapted to the Ising model on the D - dimensional cubic lattice. The state equation is solved for an arbitrary dimension D and the behavior of the free energy is analyzed. For large values of D (D > 2) the obtained results are in good agreement with the ones obtained by means of computer simulations. For small values of D, there are noticeable discrepancies with the exact results.

  20. Sustainable three-dimensional tissue model of human adipose tissue.

    PubMed

    Bellas, Evangelia; Marra, Kacey G; Kaplan, David L

    2013-10-01

    The need for physiologically relevant sustainable human adipose tissue models is crucial for understanding tissue development, disease progression, in vitro drug development and soft tissue regeneration. The coculture of adipocytes differentiated from human adipose-derived stem cells, with endothelial cells, on porous silk protein matrices for at least 6 months is reported, while maintaining adipose-like outcomes. Cultures were assessed for structure and morphology (Oil Red O content and CD31 expression), metabolic functions (leptin, glycerol production, gene expression for GLUT4, and PPARγ) and cell replication (DNA content). The cocultures maintained size and shape over this extended period in static cultures, while increasing in diameter by 12.5% in spinner flask culture. Spinner flask cultures yielded improved adipose tissue outcomes overall, based on structure and function, when compared to the static cultures. This work establishes a tissue model system that can be applied to the development of chronic metabolic dysfunction systems associated with human adipose tissue, such as obesity and diabetes, due to the long term sustainable functions demonstrated here.

  1. Weyl Phases in a Three Dimensional Network Model

    NASA Astrophysics Data System (ADS)

    Wang, Hailong; Chong, Yidong; theoretical photonics Team

    We study the topological properties of 3D ``Floquet'' band structures, defined using unitary evolution matrices rather than Hamiltonians. Such band structures can be realized in coherent-wave networks or lattices subjected to time-periodic drives. Previously, 2D Floquet band structures have been shown to exhibit unusual topological behaviors such as topologically-nontrivial zero-Chern-number phases. Here, we analyze the Floquet band structure of a 3D network model, which exhibits an Floquet analogue of a Weyl phase. The surface states exhibit topologically-protected ``Fermi'' arcs, similar to the recently-discovered Weyl semi-metals; however, the Weyl points in different quasi-energy gaps are related by a particle-hole symmetry which is unique to the Floquet system. By tuning the coupling parameters of the network, we can drive a transition between conventional insulator, weak topological insulator, and Weyl phases. Finally, we discuss the possibility of realizing this model using custom-designed electromagnetic networks. GRANT: Supported by Singapore National Research Foundation under Grant No. NRFF2012-02.

  2. Computer modeling of a three-dimensional steam injection experiment

    SciTech Connect

    Joshi, S.; Castanier, L.M.

    1993-08-01

    The experimental results and CT scans obtained during a steam-flooding experiment with the SUPRI 3-D steam injection laboratory model are compared with the results obtained from a numerical simulator for the same experiment. Simulation studies were carried out using the STARS (Steam and Additives Reservoir Simulator) compositional simulator. The saturation and temperature distributions obtained and heat-loss rates measured in the experimental model at different stages of steam-flooding were compared with those calculated from the numerical simulator. There is a fairly good agreement between the experimental results and the simulator output. However, the experimental scans show a greater degree of gravity override than that obtained with the simulator for the same heat-loss rates. Symmetric sides of the experimental 5-spot show asymmetric heat-loss rates contrary to theory and simulator results. Some utility programs have been written for extracting, processing and outputting the required grid data from the STARS simulator. These are general in nature and can be useful for other STARS users.

  3. Three-Dimensional Human Tissue Models of Wounded Skin

    PubMed Central

    Egles, Christophe; Garlick, Jonathan A.; Shamis, Yulia

    2010-01-01

    Human skin equivalents (HSEs) are in vitro tissues in which a fully differentiated, stratified squamous epithelium is grown at an air–liquid interface on a Type I collagen gel harboring human dermal fibroblasts. HSEs now provide experimental human tissue models to study factors that direct re-epithelialization and epithelial–mesenchymal cross-talk following wounding. This chapter describes the fabrication of HSEs from human keratinocytes and fibroblasts and how HSEs can be modified to characterize the response of the human epithelium during wound repair. The protocols outlined first describe techniques for the generation of human tissues that closely approximate the architectural features, differentiation, and growth of human skin. This will be followed by a description of a protocol that enables HSEs to be adapted to monitor their response following wounding. These engineered human tissues provide powerful tools to study biological process in tissues that mimic the healing of human skin and of the epithelial tissue. PMID:19908015

  4. Three-dimensional ovarian cancer models: imaging and therapeutic combinations

    NASA Astrophysics Data System (ADS)

    Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan; Hasan, Tayyaba

    2010-02-01

    We introduce a new platform to study treatment response in adherent micrometastatic ovarian cancer, combining an in vitro 3D model, with custom quantitative analysis routines to report growth and cytotoxic response in large sets of image data. OVCAR-5 human ovarian cancer cells were grown on a bed of Growth Factor Reduced MatrigelTM (GFR MatrigelTM). Using batch analysis routines to analyze longitudinal image data we show that in vitro tumor growth leads to a reproducible log-normal size distribution with two well-defined peaks. These distinct growth modes correspond to a population with approximately constant diameter of 20μm over the time probed, while the other peak corresponds to a more rapidly assembling sub-distribution of micronodules which shifts towards larger peak center positions with mean equivalent diameters of 92μm, 120μm and 150μm at days 7, 10 and 17 following plating. At day 10, 3D and monolayer cultures were treated with a regimen of either carboplatin or photodynamic therapy. Using a quantitative fluorescence imaging approach we report dose response curves and demonstrate that 3D nodules are significantly less sensitive to treatment than the same cells grown in monolayer. 3D cultures subject to 5J/cm2 PDT (250nM BPD-MA) exhibited a mean viability of 80% (95% CI = 73% to 82%) relative to no treatment control. 3D cultures subject to carboplatin treatment at 100μM concentration exhibited a mean viability of 92% (95% CI =86% to 97%). A combination treatment of 5J/cm2 PDT followed by 100μM carboplatin yielded an enhanced cytotoxic effect with mean viability of 46%, 95% confidence interval (CI) = (35 % to 46%).

  5. Three Dimensional Large Eddy Simulation Model of Turbulence in a Meandering Channel

    NASA Astrophysics Data System (ADS)

    Akahori, R.; Schmeeckle, M. W.

    2002-12-01

    Recent research has shown that intermittency caused by large-scale turbulence structures in rivers can be critical to accurate prediction of the sediment transport field. These large-scale turbulence structures are inherently three-dimensional. This is especially true in a river meander where strong secondary flows affect not only the three-dimensional, time-averaged flow structure, but also the process of large-scale turbulent eddy generation. It is very difficult to directly measure the turbulence field in a river except at the water surface or a few points in the interior of the flow. Numerical simulation of turbulence is a powerful tool, because it can provide information about the non-averaged flow at each grid point. Many previous researchers have calculated the time-averaged flow in a meandering channel, and obtained useful results. However, simulations of turbulence in meandering channels have been restricted to two dimensions. Therefore, they have a problem in accurately reproducing important features of the flow. We present a 3-dimenstional turbulent model for the numerical calculation of channel flow. The turbulence cannot be resolved at scales smaller than the channel grid, and we therefore parameterize the effects of small scale turbulence using standard Large Eddy Simulation (LES) assumptions. A Body Fitted Coordinate (BFC) system is employed to fit the irregular boundaries of natural channels. To solve the Navier-Stokes equations on the finite difference mesh, we employ the Cubic-Interpolated Propagation (CIP) method. The CIP method precisely solves the convective acceleration terms without numerical diffusion.

  6. Three-dimensional modeling of radiative disks in binaries

    NASA Astrophysics Data System (ADS)

    Picogna, G.; Marzari, F.

    2013-08-01

    Context. Circumstellar disks in binaries are perturbed by the companion gravity causing significant alterations of the disk morphology. Spiral waves due to the companion tidal force also develop in the vertical direction and affect the disk temperature profile. These effects may significantly influence the process of planet formation. Aims: We perform 3D numerical simulations of disks in binaries with different initial dynamical configurations and physical parameters. Our goal is to investigate their evolution and their propensity to grow planets. Methods: We use an improved version of the SPH code VINE modified to better account for momentum and energy conservation via variable smoothing and softening length. The energy equation includes a flux-limited radiative transfer algorithm. The disk cooling is obtained with the use of "boundary particles" populating the outer surfaces of the disk and radiating to infinity. We model a system made of star/disk + star/disk where the secondary star (and relative disk) is less massive than the primary. Results: The numerical simulations performed for different values of binary separation and disk density show that trailing spiral shock waves develop when the stars approach their pericenter. Strong hydraulic jumps occur at the shock front, in particular for small separation binaries, creating breaking waves, and a consistent mass stream between the two disks. Both shock waves and mass transfer cause significant heating of the disk. At apocenter these perturbations are reduced and the disks are cooled down and less eccentric. Conclusions: The disk morphology is substantially affected by the companion perturbations, in particular in the vertical direction. The hydraulic jumps may slow down or even halt the dust coagulation process. The disk is significantly heated up by spiral waves and mass transfer, and the high gas temperature may prevent the ice condensation by moving the "snow line" outward. The disordered motion triggered by

  7. Three-Dimensional Electron Optics Model Developed for Traveling-Wave Tubes

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    2000-01-01

    A three-dimensional traveling-wave tube (TWT) electron beam optics model including periodic permanent magnet (PPM) focusing has been developed at the NASA Glenn Research Center at Lewis Field. This accurate model allows a TWT designer to develop a focusing structure while reducing the expensive and time-consuming task of building the TWT and hot-testing it (with the electron beam). In addition, the model allows, for the first time, an investigation of the effect on TWT operation of the important azimuthally asymmetric features of the focusing stack. The TWT is a vacuum device that amplifies signals by transferring energy from an electron beam to a radiofrequency (RF) signal. A critically important component is the focusing structure, which keeps the electron beam from diverging and intercepting the RF slow wave circuit. Such an interception can result in excessive circuit heating and decreased efficiency, whereas excessive growth in the beam diameter can lead to backward wave oscillations and premature saturation, indicating a serious reduction in tube performance. The most commonly used focusing structure is the PPM stack, which consists of a sequence of cylindrical iron pole pieces and opposite-polarity magnets. Typically, two-dimensional electron optics codes are used in the design of magnetic focusing devices. In general, these codes track the beam from the gun downstream by solving equations of motion for the electron beam in static-electric and magnetic fields in an azimuthally symmetric structure. Because these two-dimensional codes cannot adequately simulate a number of important effects, the simulation code MAFIA (solution of Maxwell's equations by the Finite-Integration-Algorithm) was used at Glenn to develop a three-dimensional electron optics model. First, a PPM stack was modeled in three dimensions. Then, the fields obtained using the magnetostatic solver were loaded into a particle-in-cell solver where the fully three-dimensional behavior of the beam

  8. The Three-Dimensional Finite-Volume Non-Hydrostatic Icosahedral Model (NIM)

    NASA Astrophysics Data System (ADS)

    Lee, J. L.; MacDonald, A. E.

    2014-12-01

    A multi-scales Non-hydrostatic Icosahedral Model (NIM) has been developed at Earth System Research Laboratory (ESRL) to meet NOAA's future prediction mission ranging from mesoscale short-range, high-impact weather forecasts to longer-term intra-seasonal climate prediction. NIM formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM is designed to utilize the state-of-art computing architecture such as Graphic Processing Units (GPU) processors to run globally at kilometer scale resolution to explicitly resolve convective storms and complex terrains. The novel features of NIM numerical design include: 1.1. A local coordinate system upon which finite-volume integrations are undertaken. The use of a local Cartesian coordinate greatly simplifies the mathematic formulation of the finite-volume operators and leads to the finite-volume integration along straight lines on the plane, rather than along curved lines on the spherical surface. 1.2. A general indirect addressing scheme developed for modeling on irregular grid. It arranges the icosahedral grid with a one-dimensional vector loop structure, table specified memory order, and an indirect addressing scheme that yields very compact code despite the complexities of this grid. 1.3. Use of three-dimensional finite-volume integration over control volumes constructed on the height coordinates. Three-dimensional finite-volume integration accurately represents the Newton Third Law over terrain and improves pressure gradient force over complex terrain. 1.4. Use of the Runge-Kutta 4th order conservative and positive-definite transport scheme 1.5. NIM dynamical solver has been implemented on CPU as well as GPU. As one of the potential candidates for NWS next generation models, NIM dynamical core has been successfully verified with various benchmark test cases including those proposed by DCMIP

  9. A semi-implicit finite difference model for three-dimensional tidal circulation,

    USGS Publications Warehouse

    Casulli, V.; Cheng, R.T.

    1992-01-01

    A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is presented. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that in the absence of horizontal viscosity the resulting algorithm is unconditionally stable at a minimal computational cost. When only one vertical layer is specified this method reduces, as a particular case, to a semi-implicit scheme for the solutions of the corresponding two-dimensional shallow water equations. The resulting two- and three-dimensional algorithm is fast, accurate and mass conservative. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers.

  10. A three-dimensional finite element model for biomechanical analysis of the hip.

    PubMed

    Chen, Guang-Xing; Yang, Liu; Li, Kai; He, Rui; Yang, Bin; Zhan, Yan; Wang, Zhi-Jun; Yu, Bing-Nin; Jian, Zhe

    2013-11-01

    The objective of this study was to construct a three-dimensional (3D) finite element model of the hip. The images of the hip were obtained from Chinese visible human dataset. The hip model includes acetabular bone, cartilage, labrum, and bone. The cartilage of femoral head was constructed using the AutoCAD and Solidworks software. The hip model was imported into ABAQUS analysis system. The contact surface of the hip joint was meshed. To verify the model, the single leg peak force was loaded, and contact area of the cartilage and labrum of the hip and pressure distribution in these structures were observed. The constructed 3D hip model reflected the real hip anatomy. Further, this model reflected biomechanical behavior similar to previous studies. In conclusion, this 3D finite element hip model avoids the disadvantages of other construction methods, such as imprecision of cartilage construction and the absence of labrum. Further, it provides basic data critical for accurately modeling normal and abnormal loads, and the effects of abnormal loads on the hip. PMID:23504633

  11. A three-dimensional finite element model for biomechanical analysis of the hip.

    PubMed

    Chen, Guang-Xing; Yang, Liu; Li, Kai; He, Rui; Yang, Bin; Zhan, Yan; Wang, Zhi-Jun; Yu, Bing-Nin; Jian, Zhe

    2013-11-01

    The objective of this study was to construct a three-dimensional (3D) finite element model of the hip. The images of the hip were obtained from Chinese visible human dataset. The hip model includes acetabular bone, cartilage, labrum, and bone. The cartilage of femoral head was constructed using the AutoCAD and Solidworks software. The hip model was imported into ABAQUS analysis system. The contact surface of the hip joint was meshed. To verify the model, the single leg peak force was loaded, and contact area of the cartilage and labrum of the hip and pressure distribution in these structures were observed. The constructed 3D hip model reflected the real hip anatomy. Further, this model reflected biomechanical behavior similar to previous studies. In conclusion, this 3D finite element hip model avoids the disadvantages of other construction methods, such as imprecision of cartilage construction and the absence of labrum. Further, it provides basic data critical for accurately modeling normal and abnormal loads, and the effects of abnormal loads on the hip.

  12. Validation of a new method for building a three-dimensional physical model of the skull and dentition.

    PubMed

    O'Neil, M; Khambay, B; Bowman, A; Moos, K F; Barbenel, J; Walker, F; Ayoub, A

    2012-01-01

    We present a new method for replicating the skull and occlusal surface with an accurate physical model that could be used for planning orthognathic surgery. The investigation was made on 6 human skulls, and a polyvinyl splint was fabricated on the dental cast of the maxillary dentition in each case. A cone beam computed tomogram (CBCT) was taken of each skull and a three-dimensional replica produced. The distorted dentition (as a result of magnification errors and streak artefacts) was removed from the three-dimensional model and replaced by new plaster dentition that was fabricated using the polyvinyl splint and a transfer jig replication technique. To verify the accuracy of the method the human skulls and the three dimensional replica model, with the new plaster dentition in situ, were scanned using a laser scanner. The three-dimensional images produced were superimposed to identify the errors associated with the replacement of the distorted occlusal surface with the new plaster dentition. The overall mean error was 0.72 and SD was (0.26)mm. The accuracy of the method encouraged us to use it clinically in a case of pronounced facial asymmetry.

  13. Simplified three-dimensional model provides anatomical insights in lizards' caudal autotomy as printed illustration.

    PubMed

    De Amorim, Joana D C G; Travnik, Isadora; De Sousa, Bernadete M

    2015-03-01

    Lizards' caudal autotomy is a complex and vastly employed antipredator mechanism, with thorough anatomic adaptations involved. Due to its diminished size and intricate structures, vertebral anatomy is hard to be clearly conveyed to students and researchers of other areas. Three-dimensional models are prodigious tools in unveiling anatomical nuances. Some of the techniques used to create them can produce irregular and complicated forms, which despite being very accurate, lack didactical uniformity and simplicity. Since both are considered fundamental characteristics for comprehension, a simplified model could be the key to improve learning. The model here presented depicts the caudal osteology of Tropidurus itambere, and was designed to be concise, in order to be easily assimilated, yet complete, not to compromise the informative aspect. The creation process requires only basic skills in manipulating polygons in 3D modeling softwares, in addition to the appropriate knowledge of the structure to be modeled. As reference for the modeling, we used microscopic observation and a photograph database of the caudal structures. This way, no advanced laboratory equipment was needed and all biological materials were preserved for future research. Therefore, we propose a wider usage of simplified 3D models both in the classroom and as illustrations for scientific publications.

  14. Development Report on the Idaho National Laboratory Sitewide Three-Dimensional Aquifer Model

    SciTech Connect

    Thomas R. Wood; Catherine M. Helm-Clark; Hai Huang; Swen Magnuson; Travis McLing; Brennon Orr; Michael J. Rohe; Mitchell A. Plummer; Robert Podgorney; Erik Whitmore; Michael S. Roddy

    2007-09-01

    A sub-regional scale, three-dimensional flow model of the Snake River Plain Aquifer was developed to support remediation decisions for Waste Area Group 10, Operable Unit 10 08 at the Idaho National Laboratory (INL) Site. This model has been calibrated primarily to water levels and secondarily to groundwater velocities interpreted from stable isotope disequilibrium studies and the movement of anthropogenic contaminants in the aquifer from facilities at the INL. The three-dimensional flow model described in this report is one step in the process of constructing a fully three-dimensional groundwater flow and contaminant transport model as prescribed in the Idaho National Engineering and Environmental Laboratory Operable Unit 10-08 Sitewide Groundwater Model Work Plan. An updated three-dimensional hydrogeologic conceptual model is presented along with the geologic basis for the conceptual model. Sediment-dominated three-dimensional volumes were used to represent the geology and constrain groundwater flow as part of the conceptual model. Hydrological, geochemical, and geological data were summarized and evaluated to infer aquifer behavior. A primary observation from development and evaluation of the conceptual model was that relative to flow on a regional scale, the aquifer can be treated with steady-state conditions. Boundary conditions developed for the three-dimensional flow model are presented along with inverse simulations that estimate parameterization of hydraulic conductivity. Inverse simulations were performed using the pilot-point method to estimate permeability distributions. Thermal modeling at the regional aquifer scale and at the sub-regional scale using the inverted permeabilities is presented to corroborate the results of the flow model. The results from the flow model show good agreement with simulated and observed water levels almost always within 1 meter. Simulated velocities show generally good agreement with some discrepancies in an interpreted low

  15. Three-dimensional conceptual model for the Hanford Site unconfined aquifer system, FY 1993 status report

    SciTech Connect

    Thorne, P.D.; Chamness, M.A.; Spane, F.A. Jr.; Vermeul, V.R.; Webber, W.D.

    1993-12-01

    The ground water underlying parts of the Hanford Site (Figure 1.1) contains radioactive and chemical contaminants at concentrations exceeding regulatory standards (Dresel et al. 1993). The Hanford Site Ground-Water Surveillance Project, operated by Pacific Northwest Laboratory (PNL), is responsible for monitoring the movement of these contaminants to ensure that public health and the environment are protected. To support the monitoring effort, a sitewide three-dimensional ground-water flow model is being developed. This report provides an update on the status of the conceptual model that will form the basis for constructing a numerical three-dimensional flow model for, the site. Thorne and Chamness (1992) provide additional information on the initial development of the three-dimensional conceptual model.

  16. Creating physically-based three-dimensional microstructures: Bridging phase-field and crystal plasticity models.

    SciTech Connect

    Lim, Hojun; Owen, Steven J.; Abdeljawad, Fadi F.; Hanks, Byron; Battaile, Corbett Chandler

    2015-09-01

    In order to better incorporate microstructures in continuum scale models, we use a novel finite element (FE) meshing technique to generate three-dimensional polycrystalline aggregates from a phase field grain growth model of grain microstructures. The proposed meshing technique creates hexahedral FE meshes that capture smooth interfaces between adjacent grains. Three dimensional realizations of grain microstructures from the phase field model are used in crystal plasticity-finite element (CP-FE) simulations of polycrystalline a -iron. We show that the interface conformal meshes significantly reduce artificial stress localizations in voxelated meshes that exhibit the so-called "wedding cake" interfaces. This framework provides a direct link between two mesoscale models - phase field and crystal plasticity - and for the first time allows mechanics simulations of polycrystalline materials using three-dimensional hexahedral finite element meshes with realistic topological features.

  17. 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

  18. Accurate spike estimation from noisy calcium signals for ultrafast three-dimensional imaging of large neuronal populations in vivo

    PubMed Central

    Deneux, Thomas; Kaszas, Attila; Szalay, Gergely; Katona, Gergely; Lakner, Tamás; Grinvald, Amiram; Rózsa, Balázs; Vanzetta, Ivo

    2016-01-01

    Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo. PMID:27432255

  19. A three-dimensional digital visualization model of cervical nerves in a healthy person.

    PubMed

    Cao, Jiaming; Fu, Dong; Li, Sen

    2013-07-15

    Three-dimensional reconstruction nerve models are classically obtained from two-dimensional ages of "visible human" frozen sections. However, because of the flexibility of nerve tissues and small color differences compared with surrounding tissues, the integrity and validity of nerve tissues can be impaired during milling. Thus, in the present study, we obtained two-dimensional data from a healthy volunteer based on continuous CT angiography and magnetic resonance myelography. Semi-automatic segmentation and reconstruction were then conducted at different thresholds in different tissues using Mimics software. Small anatomical structures such as muscles and cervical nerves were reconstructed using the medical computer aided design module. Three-dimensional digital models of the cervical nerves and their surrounding structures were successfully developed, which allowed visualization of the spatial relation of anatomical structures with a strong three-dimensional effect, distinct appearance, clear distribution, and good continuity, precision, and integrality. These results indicate the validity of a three-dimensional digital visualization model of healthy human cervical nerves, which overcomes the disadvantages of milling, avoids data loss, and exhibits a realistic appearance and three-dimensional image. PMID:25206491

  20. Coupled models and parallel simulations for three-dimensional full-Stokes ice sheet modeling

    SciTech Connect

    Zhang, Huai; Ju, Lili; Gunzburger, Max; Ringler, Todd; Price, Stephen

    2011-01-01

    A three-dimensional full-Stokes computational model is considered for determining the dynamics, temperature, and thickness of ice sheets. The governing thermomechanical equations consist of the three-dimensional full-Stokes system with nonlinear rheology for the momentum, an advective-diffusion energy equation for temperature evolution, and a mass conservation equation for icethickness changes. Here, we discuss the variable resolution meshes, the finite element discretizations, and the parallel algorithms employed by the model components. The solvers are integrated through a well-designed coupler for the exchange of parametric data between components. The discretization utilizes high-quality, variable-resolution centroidal Voronoi Delaunay triangulation meshing and existing parallel solvers. We demonstrate the gridding technology, discretization schemes, and the efficiency and scalability of the parallel solvers through computational experiments using both simplified geometries arising from benchmark test problems and a realistic Greenland ice sheet geometry.

  1. Thrust Production and Wake Structure of an Actuated Three-Dimensional Manta Ray Model

    NASA Astrophysics Data System (ADS)

    Clark, Rick; Yungster, Nir; Smits, Alexander

    2004-11-01

    Thrust generation and wake structure is studied for a flexible manta ray model. The three-dimensional model is actuated periodically to produce a streamwise traveling wave, where the phase of the wave varies with spanwise distance. Mechanical actuators are used to achieve this deformation. The flow field is investigated using DPIV and flow visualization for a range of Strouhal numbers based on peak-to-peak amplitude of the trailing edge. The vortex kinematics in the spanwise and streamwise planes are examined, and a three-dimensional unsteady vortex model of the wake will be discussed.

  2. A three-dimensional tunnel model for calculation of train-induced ground vibration

    NASA Astrophysics Data System (ADS)

    Forrest, J. A.; Hunt, H. E. M.

    2006-07-01

    The frequency range of interest for ground vibration from underground urban railways is approximately 20 to 100 Hz. For typical soils, the wavelengths of ground vibration in this frequency range are of the order of the spacing of train axles, the tunnel diameter and the distance from the tunnel to nearby building foundations. For accurate modelling, the interactions between these entities therefore have to be taken into account. This paper describes an analytical three-dimensional model for the dynamics of a deep underground railway tunnel of circular cross-section. The tunnel is conceptualised as an infinitely long, thin cylindrical shell surrounded by soil of infinite radial extent. The soil is modelled by means of the wave equations for an elastic continuum. The coupled problem is solved in the frequency domain by Fourier decomposition into ring modes circumferentially and a Fourier transform into the wavenumber domain longitudinally. Numerical results for the tunnel and soil responses due to a normal point load applied to the tunnel invert are presented. The tunnel model is suitable for use in combination with track models to calculate the ground vibration due to excitation by running trains and to evaluate different track configurations.

  3. Experimental analysis and numerical modeling of mollusk shells as a three dimensional integrated volume.

    PubMed

    Faghih Shojaei, M; Mohammadi, V; Rajabi, H; Darvizeh, A

    2012-12-01

    In this paper, a new numerical technique is presented to accurately model the geometrical and mechanical features of mollusk shells as a three dimensional (3D) integrated volume. For this purpose, the Newton method is used to solve the nonlinear equations of shell surfaces. The points of intersection on the shell surface are identified and the extra interior parts are removed. Meshing process is accomplished with respect to the coordinate of each point of intersection. The final 3D generated mesh models perfectly describe the spatial configuration of the mollusk shells. Moreover, the computational model perfectly matches with the actual interior geometry of the shells as well as their exterior architecture. The direct generation technique is employed to generate a 3D finite element (FE) model in ANSYS 11. X-ray images are taken to show the close similarity of the interior geometry of the models and the actual samples. A scanning electron microscope (SEM) is used to provide information on the microstructure of the shells. In addition, a set of compression tests were performed on gastropod shell specimens to obtain their ultimate compressive strength. A close agreement between experimental data and the relevant numerical results is demonstrated. PMID:23137621

  4. Adaptation of an articulated fetal skeleton model to three-dimensional fetal image data

    NASA Astrophysics Data System (ADS)

    Klinder, Tobias; Wendland, Hannes; Wachter-Stehle, Irina; Roundhill, David; Lorenz, Cristian

    2015-03-01

    The automatic interpretation of three-dimensional fetal images poses specific challenges compared to other three-dimensional diagnostic data, especially since the orientation of the fetus in the uterus and the position of the extremities is highly variable. In this paper, we present a comprehensive articulated model of the fetal skeleton and the adaptation of the articulation for pose estimation in three-dimensional fetal images. The model is composed out of rigid bodies where the articulations are represented as rigid body transformations. Given a set of target landmarks, the model constellation can be estimated by optimization of the pose parameters. Experiments are carried out on 3D fetal MRI data yielding an average error per case of 12.03+/-3.36 mm between target and estimated landmark positions.

  5. Development of a three-dimensional time-dependent flow field model

    NASA Technical Reports Server (NTRS)

    Farmer, R. C.; Waldrop, W. R.; Pitts, F. H.; Shah, K. R.

    1975-01-01

    A three-dimensional, time-dependent mathematical model to represent Mobile Bay was developed. Computer programs were developed which numerically solve the appropriate conservation equations for predicting bay and estuary flow fields. The model is useful for analyzing the dispersion of sea water into fresh water and the transport of sediment, and for relating field and physical model data.

  6. Cattaneo-Christov Heat Flux Model for MHD Three-Dimensional Flow of Maxwell Fluid over a Stretching Sheet

    PubMed Central

    Rubab, Khansa; Mustafa, M.

    2016-01-01

    This letter investigates the MHD three-dimensional flow of upper-convected Maxwell (UCM) fluid over a bi-directional stretching surface by considering the Cattaneo-Christov heat flux model. This model has tendency to capture the characteristics of thermal relaxation time. The governing partial differential equations even after employing the boundary layer approximations are non linear. Accurate analytic solutions for velocity and temperature distributions are computed through well-known homotopy analysis method (HAM). It is noticed that velocity decreases and temperature rises when stronger magnetic field strength is accounted. Penetration depth of temperature is a decreasing function of thermal relaxation time. The analysis for classical Fourier heat conduction law can be obtained as a special case of the present work. To our knowledge, the Cattaneo-Christov heat flux model law for three-dimensional viscoelastic flow problem is just introduced here. PMID:27093542

  7. Cattaneo-Christov Heat Flux Model for MHD Three-Dimensional Flow of Maxwell Fluid over a Stretching Sheet.

    PubMed

    Rubab, Khansa; Mustafa, M

    2016-01-01

    This letter investigates the MHD three-dimensional flow of upper-convected Maxwell (UCM) fluid over a bi-directional stretching surface by considering the Cattaneo-Christov heat flux model. This model has tendency to capture the characteristics of thermal relaxation time. The governing partial differential equations even after employing the boundary layer approximations are non linear. Accurate analytic solutions for velocity and temperature distributions are computed through well-known homotopy analysis method (HAM). It is noticed that velocity decreases and temperature rises when stronger magnetic field strength is accounted. Penetration depth of temperature is a decreasing function of thermal relaxation time. The analysis for classical Fourier heat conduction law can be obtained as a special case of the present work. To our knowledge, the Cattaneo-Christov heat flux model law for three-dimensional viscoelastic flow problem is just introduced here. PMID:27093542

  8. Three-dimensional dynamic contrast-enhanced MRI for the accurate, extensive quantification of microvascular permeability in atherosclerotic plaques.

    PubMed

    Calcagno, Claudia; Lobatto, Mark E; Dyvorne, Hadrien; Robson, Philip M; Millon, Antoine; Senders, Max L; Lairez, Olivier; Ramachandran, Sarayu; Coolen, Bram F; Black, Alexandra; Mulder, Willem J M; Fayad, Zahi A

    2015-10-01

    Atherosclerotic plaques that cause stroke and myocardial infarction are characterized by increased microvascular permeability and inflammation. Dynamic contrast-enhanced MRI (DCE-MRI) has been proposed as a method to quantify vessel wall microvascular permeability in vivo. Until now, most DCE-MRI studies of atherosclerosis have been limited to two-dimensional (2D) multi-slice imaging. Although providing the high spatial resolution required to image the arterial vessel wall, these approaches do not allow the quantification of plaque permeability with extensive anatomical coverage, an essential feature when imaging heterogeneous diseases, such as atherosclerosis. To our knowledge, we present the first systematic evaluation of three-dimensional (3D), high-resolution, DCE-MRI for the extensive quantification of plaque permeability along an entire vascular bed, with validation in atherosclerotic rabbits. We compare two acquisitions: 3D turbo field echo (TFE) with motion-sensitized-driven equilibrium (MSDE) preparation and 3D turbo spin echo (TSE). We find 3D TFE DCE-MRI to be superior to 3D TSE DCE-MRI in terms of temporal stability metrics. Both sequences show good intra- and inter-observer reliability, and significant correlation with ex vivo permeability measurements by Evans Blue near-infrared fluorescence (NIRF). In addition, we explore the feasibility of using compressed sensing to accelerate 3D DCE-MRI of atherosclerosis, to improve its temporal resolution and therefore the accuracy of permeability quantification. Using retrospective under-sampling and reconstructions, we show that compressed sensing alone may allow the acceleration of 3D DCE-MRI by up to four-fold. We anticipate that the development of high-spatial-resolution 3D DCE-MRI with prospective compressed sensing acceleration may allow for the more accurate and extensive quantification of atherosclerotic plaque permeability along an entire vascular bed. We foresee that this approach may allow for

  9. Theory for the three-dimensional Mercedes-Benz model of water

    PubMed Central

    Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A.

    2009-01-01

    The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the “right answer,” we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim’s Ornstein–Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation. PMID:19929057

  10. Theory for the three-dimensional Mercedes-Benz model of water.

    PubMed

    Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A

    2009-11-21

    The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.

  11. Theory for the three-dimensional Mercedes-Benz model of water

    NASA Astrophysics Data System (ADS)

    Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A.

    2009-11-01

    The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation.

  12. Virtual cerebral ventricular system: an MR-based three-dimensional computer model.

    PubMed

    Adams, Christina M; Wilson, Timothy D

    2011-01-01

    The inherent spatial complexity of the human cerebral ventricular system, coupled with its deep position within the brain, poses a problem for conceptualizing its anatomy. Cadaveric dissection, while considered the gold standard of anatomical learning, may be inadequate for learning the anatomy of the cerebral ventricular system; even with intricate dissection, ventricular structures remain difficult to observe. Three-dimensional (3D) computer reconstruction of the ventricular system offers a solution to this problem. This study aims to create an accurate 3D computer reconstruction of the ventricular system with surrounding structures, including the brain and cerebellum, using commercially available 3D rendering software. Magnetic resonance imaging (MRI) scans of a male cadaver were segmented using both semiautomatic and manual tools. Segmentation involves separating voxels of different grayscale values to highlight specific neural structures. User controls enable adding or removing of structures, altering their opacity, and making cross-sectional slices through the model to highlight inner structures. Complex physiologic concepts, such as the flow of cerebrospinal fluid, are also shown using the 3D model of the ventricular system through a video animation. The model can be projected stereoscopically, to increase depth perception and to emphasize spatial relationships between anatomical structures. This model is suited for both self-directed learning and classroom teaching of the 3D anatomical structure and spatial orientation of the ventricles, their connections, and their relation to adjacent neural and skeletal structures. PMID:21976457

  13. Theory for the three-dimensional Mercedes-Benz model of water.

    PubMed

    Bizjak, Alan; Urbic, Tomaz; Vlachy, Vojko; Dill, Ken A

    2009-11-21

    The two-dimensional Mercedes-Benz (MB) model of water has been widely studied, both by Monte Carlo simulations and by integral equation methods. Here, we study the three-dimensional (3D) MB model. We treat water as spheres that interact through Lennard-Jones potentials and through a tetrahedral Gaussian hydrogen bonding function. As the "right answer," we perform isothermal-isobaric Monte Carlo simulations on the 3D MB model for different pressures and temperatures. The purpose of this work is to develop and test Wertheim's Ornstein-Zernike integral equation and thermodynamic perturbation theories. The two analytical approaches are orders of magnitude more efficient than the Monte Carlo simulations. The ultimate goal is to find statistical mechanical theories that can efficiently predict the properties of orientationally complex molecules, such as water. Also, here, the 3D MB model simply serves as a useful workbench for testing such analytical approaches. For hot water, the analytical theories give accurate agreement with the computer simulations. For cold water, the agreement is not as good. Nevertheless, these approaches are qualitatively consistent with energies, volumes, heat capacities, compressibilities, and thermal expansion coefficients versus temperature and pressure. Such analytical approaches offer a promising route to a better understanding of water and also the aqueous solvation. PMID:19929057

  14. Grid Generator for Two, Three-dimensional Finite Element Subsurface Flow Models

    1993-04-28

    GRIDMAKER serves as a preprocessor for finite element models in solving two- and three-dimensional subsurface flow and pollutant transport problems. It is designed to generate three-point triangular or four-point quadrilateral elements for two-dimensional domains and eight-point hexahedron elements for three-dimensional domains. A two-dimensional domain of an aquifer with a variable depth layer is treated as a special case for depth-integrated two-dimensional, finite element subsurface flow models. The program accommodates the need for aquifers with heterogeneousmore » systems by identifying the type of material in each element.« less

  15. GRIDMAKER. Grid Generator for Two, Three-dimensional Finite Element Subsurface Flow Models

    SciTech Connect

    Tsay, T.K.; Yeh, G.T.; Wilson, G.V.; Toran, L.E.

    1990-06-01

    GRIDMAKER serves as a preprocessor for finite element models in solving two- and three-dimensional subsurface flow and pollutant transport problems. It is designed to generate three-point triangular or four-point quadrilateral elements for two-dimensional domains and eight-point hexahedron elements for three-dimensional domains. A two-dimensional domain of an aquifer with a variable depth layer is treated as a special case for depth-integrated two-dimensional, finite element subsurface flow models. The program accommodates the need for aquifers with heterogeneous systems by identifying the type of material in each element.

  16. Evaluation of geographic information systems for three-dimensional ground-water modeling, Yucca Mountain, Nevada

    USGS Publications Warehouse

    Turner, A. Keith; Ervin, Elisabeth M.; Downey, Joe S.

    1991-01-01

    Fully three-dimensional representations of the geologic system at Yucca Mountain have been developed using a Geoscientific Information System, which is an expansion of a traditional Geographic Information Systems. These advanced, three dimensional, representations of Yucca Mountain are required to adequately evaluate the complex geologic and hydrologic conditions surrounding the site. This Geoscientific Information System will be used to store, analyze, and display site data. The system also will provide a link between geologic and hydrologic data and the numerical ground-water-flow model resulting in more easy testing of hypotheses concerning the conceptual model of the geohydrologic system at Yucca Mountain.

  17. Modeling Dispersion of Chemical-Biological Agents in Three Dimensional Living Space

    SciTech Connect

    William S. Winters

    2002-02-01

    This report documents a series of calculations designed to demonstrate Sandia's capability in modeling the dispersal of chemical and biological agents in complex three-dimensional spaces. The transport of particles representing biological agents is modeled in a single room and in several connected rooms. The influence of particle size, particle weight and injection method are studied.

  18. Three-dimensional numerical modeling of water quality and sediment-associated processes in natural lakes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter presents the development and application of a three-dimensional water quality model for predicting the distributions of nutrients, phytoplankton, dissolved oxygen, etc., in natural lakes. In this model, the computational domain was divided into two parts: the water column and the bed se...

  19. Transient three-dimensional thermal model for batteries with thin electrodes

    NASA Astrophysics Data System (ADS)

    Taheri, Peyman; Yazdanpour, Maryam; Bahrami, Majid

    2013-12-01

    A three-dimensional analytical model is proposed to investigate the thermal response of batteries, with a plurality of thin electrodes, to heat generation during their operation. The model is based on integral-transform technique that gives a closed-form solution for the fundamental problem of unsteady heat conduction in batteries with orthotropic thermal conductivities, where the heat generation is a function of both temperature and depth-of-discharge. The full-field solutions take the form of a rapidly converging triple infinite sum whose leading terms provide a very simple yet accurate approximation of the battery thermal behavior with modest numerical effort. The accuracy of the proposed model is tested through comparison with numerical simulations. The method is used to describe spatial and temporal temperature evolution in a sample pouch type lithium-ion polymer battery during galvanostatic discharge processes while subjected to convective-radiative cooling at its surfaces (the most practical case is considered, when surrounding medium is at a constant ambient temperature). In the simulations, emphasis is placed on the maintenance of the battery operational temperature below a critical temperature. Through definition of a surface-averaged Biot number, certain conditions are highlighted, under which a two-dimensional thermal analysis is applicable.

  20. Monitoring Prostate Tumor Growth in an Orthotopic Mouse Model Using Three-Dimensional Ultrasound Imaging Technique.

    PubMed

    Ni, Jie; Cozzi, Paul; Hung, Tzong-Tyng; Hao, Jingli; Graham, Peter; Li, Yong

    2016-02-01

    Prostate cancer (CaP) is the most commonly diagnosed and the second leading cause of death from cancer in males in USA. Prostate orthotopic mouse model has been widely used to study human CaP in preclinical settings. Measurement of changes in tumor size obtained from noninvasive diagnostic images is a standard method for monitoring responses to anticancer modalities. This article reports for the first time the usage of a three-dimensional (3D) ultrasound system equipped with photoacoustic (PA) imaging in monitoring longitudinal prostate tumor growth in a PC-3 orthotopic NODSCID mouse model (n = 8). Two-dimensional and 3D modes of ultrasound show great ability in accurately depicting the size and shape of prostate tumors. PA function on two-dimensional and 3D images showed average oxygen saturation and average hemoglobin concentration of the tumor. Results showed a good fit in representative exponential tumor growth curves (n = 3; r(2) = 0.948, 0.955, and 0.953, respectively) and a good correlation of tumor volume measurements performed in vivo with autopsy (n = 8, r = 0.95, P < .001). The application of 3D ultrasound imaging proved to be a useful imaging modality in monitoring tumor growth in an orthotopic mouse model, with advantages such as high contrast, uncomplicated protocols, economical equipment, and nonharmfulness to animals. PA mode also enabled display of blood oxygenation surrounding the tumor and tumor vasculature and angiogenesis, making 3D ultrasound imaging an ideal tool for preclinical cancer research.

  1. Three-dimensional air flow model for soil venting: Superposition of analytical functions

    SciTech Connect

    Cho, J.S.

    1993-01-01

    A three-dimensional computer model was developed for the simulation of the soil-air pressure distribution at steady state and specific discharge vectors during soil venting with multiple wells in unsaturated soil. The Kirchhoff transformation of dependent variables and coordinate transforms allowed the adoption of the superposition of analytical functions to satisfy the differential equations and boundary conditions. A venting well was represented with a line source of a finite length in a infinite homogeneous medium. The boundary conditions at the soil surface and the water table were approximated by the superposition of a large number of mirror image wells on the opposite sides of boundaries. The numerical accuracy of the model was checked by the evaluation of one of the boundary conditions and the comparison of a simulation result with an available analytical solution from the literature. Simulations of various layouts of operating systems with multiple wells required minimal computational expenses. The model was very flexible and easy to use, and its numerical results proved to be sufficiently accurate.

  2. Research on three-dimensional positioning method of big data image under bag of words model guidance

    NASA Astrophysics Data System (ADS)

    Zhang, Chunsen; Wang, Xiqi; Qiu, Zhenguo; Zhu, Shihuan; Xu, Xiaolei; Zhong, Sidong

    2015-12-01

    In order to retrieve the positioning image efficiently and quickly from a large number of different images to realize the three-dimensional spatial positioning, in this article, based on photogrammetry and computer vision theory, a new method of three-dimensional positioning of big data image under the bag of words model guidance is proposed. The method consists of two parts: image retrieving and spatial positioning. First, complete image retrieval by feature extraction, K-means clustering, bag of words model building and other processes, thus improve the efficiency of image matching. Second, achieve interior and exterior orientation element through image matching, building projection relationship and calculating the projection matrix, and then the spatial orientation is realized. The experimental result showed that the proposed method can retrieve the target image efficiently and achieve spatial orientation accurately, which made a beneficial exploration for achieving space positioning based on big data images.

  3. Three-Dimensional Animation Technology: a New Interactive Model Designed for the Teaching of Cryospheric Science

    NASA Astrophysics Data System (ADS)

    Porter, P. R.; Marunchak, A.

    2011-12-01

    One of the key challenges facing educators in the cryospheric sciences is to explain to students the processes that operate and the landforms that exist in relatively unfamiliar glacial environments. In many cases these environments are also largely inaccessible which can hinder field-based teaching. This is particularly the case for en-glacial and sub-glacial hydrology and the closely related topic of sub-glacial glacier dynamics, yet a full understanding of these subject areas is pivotal to overall student understanding of glaciology. An ability to visualise these unfamiliar and inaccessible environments offers a potentially powerful tool to assist student conceptualisation and comprehension. To address this we have developed a three-dimensional interactive 'virtual glacier' simulation model. Based on standards and technology established by the rapidly evolving video gaming industry, the user is presented with an interactive real-time three-dimensional environment designed to accurately portray multiple aspects of glacial environments. The user can move in all directions in the fore-field area, on the glacier surface and within en-glacial and sub-glacial drainage networks. Descent into the glacier hydrological system is via a moulin, from which the user can explore en-glacial channels linking to this moulin and ultimately descend into the sub-glacial drainage system. Various sub-glacial drainage network morphologies can then be 'explored' to aid conceptualisation and understanding and the user can navigate through drainage networks both up- and down-glacier and ultimately emerge at the portal into the fore-field environment. Interactive icons relating to features of interest are presented to the user throughout the model, prompting multimedia dialogue boxes to open. Dialogue box content (e.g. text, links to online resources, videos, journal papers, etc.) is fully customisable by the educator. This facilitates the use of the model at different academic levels

  4. Continuous data assimilation for the three-dimensional Brinkman-Forchheimer-extended Darcy model

    NASA Astrophysics Data System (ADS)

    Markowich, Peter A.; Titi, Edriss S.; Trabelsi, Saber

    2016-04-01

    In this paper we introduce and analyze an algorithm for continuous data assimilation for a three-dimensional Brinkman-Forchheimer-extended Darcy (3D BFeD) model of porous media. This model is believed to be accurate when the flow velocity is too large for Darcy’s law to be valid, and additionally the porosity is not too small. The algorithm is inspired by ideas developed for designing finite-parameters feedback control for dissipative systems. It aims to obtain improved estimates of the state of the physical system by incorporating deterministic or noisy measurements and observations. Specifically, the algorithm involves a feedback control that nudges the large scales of the approximate solution toward those of the reference solution associated with the spatial measurements. In the first part of the paper, we present a few results of existence and uniqueness of weak and strong solutions of the 3D BFeD system. The second part is devoted to the convergence analysis of the data assimilation algorithm.

  5. Three-dimensional Wavelet-based Adaptive Mesh Refinement for Global Atmospheric Chemical Transport Modeling

    NASA Astrophysics Data System (ADS)

    Rastigejev, Y.; Semakin, A. N.

    2013-12-01

    Accurate numerical simulations of global scale three-dimensional atmospheric chemical transport models (CTMs) are essential for studies of many important atmospheric chemistry problems such as adverse effect of air pollutants on human health, ecosystems and the Earth's climate. These simulations usually require large CPU time due to numerical difficulties associated with a wide range of spatial and temporal scales, nonlinearity and large number of reacting species. In our previous work we have shown that in order to achieve adequate convergence rate and accuracy, the mesh spacing in numerical simulation of global synoptic-scale pollution plume transport must be decreased to a few kilometers. This resolution is difficult to achieve for global CTMs on uniform or quasi-uniform grids. To address the described above difficulty we developed a three-dimensional Wavelet-based Adaptive Mesh Refinement (WAMR) algorithm. The method employs a highly non-uniform adaptive grid with fine resolution over the areas of interest without requiring small grid-spacing throughout the entire domain. The method uses multi-grid iterative solver that naturally takes advantage of a multilevel structure of the adaptive grid. In order to represent the multilevel adaptive grid efficiently, a dynamic data structure based on indirect memory addressing has been developed. The data structure allows rapid access to individual points, fast inter-grid operations and re-gridding. The WAMR method has been implemented on parallel computer architectures. The parallel algorithm is based on run-time partitioning and load-balancing scheme for the adaptive grid. The partitioning scheme maintains locality to reduce communications between computing nodes. The parallel scheme was found to be cost-effective. Specifically we obtained an order of magnitude increase in computational speed for numerical simulations performed on a twelve-core single processor workstation. We have applied the WAMR method for numerical

  6. Innovations in knee arthroplasty: three-dimensional modeling and analytical technology (SOMA).

    PubMed

    Banerjee, Samik; D'Alessio, Jerry; Kester, Mark; Harwin, Steven F; Dunbar, Michael; Mont, Michael A

    2014-03-01

    The development of three-dimensional (3D) knee models and analytical tools from large databases of computerized tomographic data linked to patient demographics has led to the development of a fuller understanding of the amount of variation in the anatomy and morphology of the human knee and how this relates to clinical applications. In this study, we have aimed to review the spectrum of clinical applications of three-dimensional modeling, which includes osteotomies and knee arthroplasties. More specifically, three-dimensional modeling has been used for: the assessment of tibial and femoral morphometry, the potential development of novel instrumentation for femoral resection, the evaluation of femoral condylar anthropometry, correlating mechanical and anatomical alignment, the assessment of the relationship of joint line and flexion, the extension and mechanical axis of the knee, and the evaluation of the relationship between medial tibial tubercle to the posterior aspect of the tibia. Three-dimensional modeling and analytical technology may provide insights into anthropometric variations in the knee and may assist in the future development of more patient specific instrumentation, implant positioning, and implant designs. It is hoped that such advances could improve patient satisfaction and long-term implant survivorship.

  7. GRAVPOLY; a modification of a three-dimensional gravity modeling program

    USGS Publications Warehouse

    Godson, Richard H.

    1983-01-01

    The three-dimensional magnetic modelling program of Donald Plouff (Plouff, 1975) has been made operational on a Honeywell Multics 68/80 computer. Modifications were made to input and output procedures to make the program compatible with U.S. Geological Survey (USGS) standard geophysical input and output formats.

  8. A THREE-DIMENSIONAL AIR FLOW MODEL FOR SOIL VENTING: SUPERPOSITION OF ANLAYTICAL FUNCTIONS

    EPA Science Inventory

    A three-dimensional computer model was developed for the simulation of the soil-air pressure distribution at steady state and specific discharge vectors during soil venting with multiple wells in unsaturated soil. The Kirchhoff transformation of dependent variables and coordinate...

  9. Hydraulic fracturing model based on a three-dimensional closed form

    SciTech Connect

    Bouteca, M.J. )

    1988-11-01

    The numerical model described in this paper was designed to provide a realistic three-dimensional (3D) solution for fracture propagation in minimal computation time. Comparisons with available results show good concordance for a wide range of data. The results of a parametric study are compared with the Nolte analysis of the propagation pressure.

  10. Exact quantum cross sections for a three dimensional angle dependent model for three body reactions.

    NASA Technical Reports Server (NTRS)

    Baer, M.; Kouri, D. J.

    1971-01-01

    Exact quantum mechanical reactive cross sections are reported for a three dimensional angle dependent model surface. The surface simulates an atom-heteronuclear diatom system A + BC leading to AB + C where atom B is much heavier than A or C. The molecules BC and AB are taken to be rotating vibrators which can dissociate. Results for two angle dependent potentials are given.

  11. Three-dimensional tissue assemblies: novel models for the study of Salmonella enterica serovar Typhimurium pathogenesis

    NASA Technical Reports Server (NTRS)

    Nickerson, C. A.; Goodwin, T. J.; Terlonge, J.; Ott, C. M.; Buchanan, K. L.; Uicker, W. C.; Emami, K.; LeBlanc, C. L.; Ramamurthy, R.; Clarke, M. S.; Vanderburg, C. R.; Hammond, T.; Pierson, D. L.

    2001-01-01

    The lack of readily available experimental systems has limited knowledge pertaining to the development of Salmonella-induced gastroenteritis and diarrheal disease in humans. We used a novel low-shear stress cell culture system developed at the National Aeronautics and Space Administration in conjunction with cultivation of three-dimensional (3-D) aggregates of human intestinal tissue to study the infectivity of Salmonella enterica serovar Typhimurium for human intestinal epithelium. Immunohistochemical characterization and microscopic analysis of 3-D aggregates of the human intestinal epithelial cell line Int-407 revealed that the 3-D cells more accurately modeled human in vivo differentiated tissues than did conventional monolayer cultures of the same cells. Results from infectivity studies showed that Salmonella established infection of the 3-D cells in a much different manner than that observed for monolayers. Following the same time course of infection with Salmonella, 3-D Int-407 cells displayed minimal loss of structural integrity compared to that of Int-407 monolayers. Furthermore, Salmonella exhibited significantly lower abilities to adhere to, invade, and induce apoptosis of 3-D Int-407 cells than it did for infected Int-407 monolayers. Analysis of cytokine expression profiles of 3-D Int-407 cells and monolayers following infection with Salmonella revealed significant differences in expression of interleukin 1alpha (IL-1alpha), IL-1beta, IL-6, IL-1Ra, and tumor necrosis factor alpha mRNAs between the two cultures. In addition, uninfected 3-D Int-407 cells constitutively expressed higher levels of transforming growth factor beta1 mRNA and prostaglandin E2 than did uninfected Int-407 monolayers. By more accurately modeling many aspects of human in vivo tissues, the 3-D intestinal cell model generated in this study offers a novel approach for studying microbial infectivity from the perspective of the host-pathogen interaction.

  12. Three-Dimensional Tissue Assemblies: Novel Models for the Study of Salmonella enterica Serovar Typhimurium Pathogenesis

    PubMed Central

    Nickerson, Cheryl A.; Goodwin, Thomas J.; Terlonge, Jacqueline; Ott, C. Mark; Buchanan, Kent L.; Uicker, William C.; Emami, Kamal; LeBlanc, Carly L.; Ramamurthy, Rajee; Clarke, Mark S.; Vanderburg, Charles R.; Hammond, Timothy; Pierson, Duane L.

    2001-01-01

    The lack of readily available experimental systems has limited knowledge pertaining to the development of Salmonella-induced gastroenteritis and diarrheal disease in humans. We used a novel low-shear stress cell culture system developed at the National Aeronautics and Space Administration in conjunction with cultivation of three-dimensional (3-D) aggregates of human intestinal tissue to study the infectivity of Salmonella enterica serovar Typhimurium for human intestinal epithelium. Immunohistochemical characterization and microscopic analysis of 3-D aggregates of the human intestinal epithelial cell line Int-407 revealed that the 3-D cells more accurately modeled human in vivo differentiated tissues than did conventional monolayer cultures of the same cells. Results from infectivity studies showed that Salmonella established infection of the 3-D cells in a much different manner than that observed for monolayers. Following the same time course of infection with Salmonella, 3-D Int-407 cells displayed minimal loss of structural integrity compared to that of Int-407 monolayers. Furthermore, Salmonella exhibited significantly lower abilities to adhere to, invade, and induce apoptosis of 3-D Int-407 cells than it did for infected Int-407 monolayers. Analysis of cytokine expression profiles of 3-D Int-407 cells and monolayers following infection with Salmonella revealed significant differences in expression of interleukin 1α (IL-1α), IL-1β, IL-6, IL-1Ra, and tumor necrosis factor alpha mRNAs between the two cultures. In addition, uninfected 3-D Int-407 cells constitutively expressed higher levels of transforming growth factor β1 mRNA and prostaglandin E2 than did uninfected Int-407 monolayers. By more accurately modeling many aspects of human in vivo tissues, the 3-D intestinal cell model generated in this study offers a novel approach for studying microbial infectivity from the perspective of the host-pathogen interaction. PMID:11598087

  13. Three-dimensional modeling of an ideal nozzle for advanced propulsion

    NASA Astrophysics Data System (ADS)

    Schillo, Kevin

    Advanced propulsion systems such as pulsed fission and fusion rockets hold the potential for opening up the solar system in ways few other propulsion technologies can. The University of Alabama in Huntsville is exploring one such concept in the form of pulsed z-pinch fusion propulsion. One of the technical hurdles to utilizing any pulsed fusion concept is the conversion from an isotropic expansion of a plasma into directed motion to produce thrust. This thesis investigates three dimensional modeling of pulsed nozzle performance in which the initial gas is a cylindrical gas column, emulating the initial conditions found in pulsed plasma discharges common in fusion experiments. Two nozzle geometries were investigated, a pusher plate and a hemispherical nozzle. Simulations of these systems were conducted using SPFMax, a recently developed smoothed particle hydrodynamics code (SPH). The SPH method was chosen because it is naturally adaptive and accurate for resolving the vacuum/gas boundary which always exists in pulsed fusion systems. Argon plasma was used to compare the two systems to determine which offers better performance. The plasma was also subjected to a wide variety of shapes and initial conditions to determine what would offer higher performance for the two systems.

  14. A finite-volume ELLAM for three-dimensional solute-transport modeling

    USGS Publications Warehouse

    Russell, T.F.; Heberton, C.I.; Konikow, L.F.; Hornberger, G.Z.

    2003-01-01

    A three-dimensional finite-volume ELLAM method has been developed, tested, and successfully implemented as part of the U.S. Geological Survey (USGS) MODFLOW-2000 ground water modeling package. It is included as a solver option for the Ground Water Transport process. The FVELLAM uses space-time finite volumes oriented along the streamlines of the flow field to solve an integral form of the solute-transport equation, thus combining local and global mass conservation with the advantages of Eulerian-Lagrangian characteristic methods. The USGS FVELLAM code simulates solute transport in flowing ground water for a single dissolved solute constituent and represents the processes of advective transport, hydrodynamic dispersion, mixing from fluid sources, retardation, and decay. Implicit time discretization of the dispersive and source/sink terms is combined with a Lagrangian treatment of advection, in which forward tracking moves mass to the new time level, distributing mass among destination cells using approximate indicator functions. This allows the use of large transport time increments (large Courant numbers) with accurate results, even for advection-dominated systems (large Peclet numbers). Four test cases, including comparisons with analytical solutions and benchmarking against other numerical codes, are presented that indicate that the FVELLAM can usually yield excellent results, even if relatively few transport time steps are used, although the quality of the results is problem-dependent.

  15. Global Well-Posedness of an Inviscid Three-Dimensional Pseudo-Hasegawa-Mima Model

    NASA Astrophysics Data System (ADS)

    Cao, Chongsheng; Farhat, Aseel; Titi, Edriss S.

    2013-04-01

    The three-dimensional inviscid Hasegawa-Mima model is one of the fundamental models that describe plasma turbulence. The model also appears as a simplified reduced Rayleigh-Bénard convection model. The mathematical analysis of the Hasegawa-Mima equation is challenging due to the absence of any smoothing viscous terms, as well as to the presence of an analogue of the vortex stretching terms. In this paper, we introduce and study a model which is inspired by the inviscid Hasegawa-Mima model, which we call a pseudo-Hasegawa-Mima model. The introduced model is easier to investigate analytically than the original inviscid Hasegawa-Mima model, as it has a nicer mathematical structure. The resemblance between this model and the Euler equations of inviscid incompressible fluids inspired us to adapt the techniques and ideas introduced for the two-dimensional and the three-dimensional Euler equations to prove the global existence and uniqueness of solutions for our model. This is in addition to proving and implementing a new technical logarithmic inequality, generalizing the Brezis-Gallouet and the Brezis-Wainger inequalities. Moreover, we prove the continuous dependence on initial data of solutions for the pseudo-Hasegawa-Mima model. These are the first results on existence and uniqueness of solutions for a model that is related to the three-dimensional inviscid Hasegawa-Mima equations.

  16. Modelling canopy scale solar induced chlorophyll fluorescence simulated by the three dimensional radiative transfer model

    NASA Astrophysics Data System (ADS)

    Kobayashi, H.; Nagai, S.; Inoue, T.; Yang, W.; Ichii, K.

    2014-12-01

    Recent studies show that the vegetation canopy scale sun-induced chlorophyll fluorescence (SIF) can be observed from satellite. To understand how the canopy scale bidirectional fluorescence observations are related to three-dimensional fluorescence distribution within a plant canopy, it is necessary to evaluate canopy scale fluorescence emission using a detailed plant canopy radiative transfer model. In this study, we developed a three-dimensional plant canopy radiative transfer model that can simulate the bidirectional chlorophyll fluorescence radiance and show several preliminary results of fluorescence distribution at the tree level. To simulate the three dimensional variations in chlorophyll fluorescence from trees, we measured tree structures using a terrestrial LiDAR instrument. The measurements were conducted in Yokohama, Japan (35°22'49" N 139°37'29" E). Three Japanese cherry trees (Cerasus Speciosa) were chosen for our study (Figure 1). Leaf-level sun-induced chlorophyll fluorescence (SIF) is also necessary as an input of radiative transfer model. To measure the leaf-level SIF, we used high spectral resolution spectroradiometer (HR 4000, Ocean Optics Inc. USA). The spectral resolution of this instrument is 0.05 nm (full width half maximum). The spectral range measured was 720 to 780 nm. From the spectral radiance measurements, we estimated SIF using the three band Fraunhofer Line Depth (3FLD) method. The effect of solar and view zenith angles, multiple scattering depends on many factors such as back ground reflectance, leaf reflectance transmittance and landscape structures. To understand how the SIF from both sparse and dense forest stands vary with sun and view angles and optical variables, it is necessary to conduct further sensitivity analysis. Radiative transfer simulation will help understand SIF emission at variety of forest canopy cases.

  17. Three-dimensional eutrophication model of Chesapeake Bay. Volume 1: Main report. Final report

    SciTech Connect

    Cerco, C.F.; Cole, T.M.

    1994-05-01

    A three-dimensional, time-variable, eutrophication model, CE-QUAL-ICM, was applied to Chesapeake Bay. The model incorporated 22 state variables that included physical properties, multiple forms of algae, carbon, nitrogen, phosphorus, and silica, and dissolved oxygen. The model was part of a larger package that included a three-dimensional hydrodynamic model and a benthic sediment diagenesis model. The model was initially applied to a 3-year period, 1984-1986. The model successfully simulated water-column and sediment processes that affected water quality. Phenomena simulated include formation of the spring algal bloom subsequent to the annual peak in nutrient runoff, onset and breakup of summer anoxia, and coupling of organic particle deposition with sediment-water nutrient and oxygen fluxes. The model was next applied in a 30-year simulation of water quality, 1959-1988. The model indicated longterm trends in water quality and affirmed the role of stratification in determining anoxia. Final application of the model was in a series of nutrient load-reduction sensitivity analyses. The study demonstrated that complex eutrophication problems can be addressed with coupled three-dimensional hydrodynamic and water quality models.

  18. Ozone and other trace gases in the Arctic and Antarctic regions: Three-dimensional model simulations

    SciTech Connect

    Granier, C.; Brasseur, G. )

    1991-02-20

    A three-dimensional mechanistic model of the middle atmosphere with calculated dynamics and chemistry is used to study the behavior of chemically active trace gases at high latitudes in winter and spring, and to simulate the formation of an ozone hole in Antarctica. The dynamics of both hemispheres is simulated by applying at the lower boundary of the model (8.5 km) a wavelike perturbation representing qualitatively a climatological tropospheric forcing. The chemical heterogeneous processes converting chlorine reservoirs into active chlorine in cold air masses are parameterized. The model simulates the behavior of nitrogen oxides, nitric acid, water vapor, methane, hydrogen radicals, chlorine compounds, and ozone. It reproduces important features observed during different Antarctic and Arctic observation campaigns. The ozone hole in the southern hemisphere can only be simulated when the heterogeneous polar chemistry is taken into account. The springtime ozone depletion over Antarctica calculated in the model is thus mostly the result of chemical removal although the dynamics is responsible for the low temperature that triggers the large ozone loss rates. Unresolved questions are related to the strength of the vertical exchanges inside the vortex, the preconditioning of trace gases before and during the winter season, the behavior of the different trace gases as the vortex breaks down (dilution effects), accurate determination of the ozone sink inside the vortex, and a better quantitative estimation of the role of polar stratospheric clouds. Despite elevated concentrations of active chlorine at high latitudes in the northern hemisphere in late winter, no ozone hole is produced by the model, even with chlorine levels as high as 6 ppbv. This conclusion could, however, be modified for very stable and cold winters with delayed final warming.

  19. Computational modeling of phonatory dynamics in a tubular three-dimensional model of the human larynx

    PubMed Central

    Xue, Q.; Mittal, R.; Zheng, X.; Bielamowicz, S.

    2012-01-01

    Simulation of the phonatory flow-structure interaction has been conducted in a three-dimensional, tubular shaped laryngeal model that has been designed with a high level of realism with respect to the human laryngeal anatomy. A non-linear spring-based contact force model is also implemented for the purpose of representing contact in more general conditions, especially those associated with three-dimensional modeling of phonation in the presence of vocal fold pathologies. The model is used to study the effects of a moderate (20%) vocal-fold tension imbalance on the phonatory dynamics. The characteristic features of phonation for normal as well as tension-imbalanced vocal folds, such as glottal waveform, glottal jet evolution, mucosal wave-type vocal-fold motion, modal entrainment, and asymmetric glottal jet deflection have been discussed in detail and compared to established data. It is found that while a moderate level of tension asymmetry does not change the vibratory dynamics significantly, it can potentially lead to measurable deterioration in voice quality. PMID:22978889

  20. Modelling of three-dimensional shock wave turbulent boundary layer interactions

    NASA Astrophysics Data System (ADS)

    Knight, D. D.

    The accuracy of numerical computations of the three-dimensional sharp fin flow field using the Reynolds-averaged Navier-Stokes equations is examined. Computed flows are compared with a set of benchmark experiments at Mach 3 for two different Reynolds numbers. A detailed comparison is performed between experimental data and separate computational results for the three-dimensional sharp fin for a 10 deg fin angle in order to examine the accuracy of two different turbulence models. The computed surface pressure for the fin at a 20 deg angle is compared with recent experimental data. The computed yaw angle profiles are shown to be sensitive to the turbulence model. In the immediate vicinity of the surface, the calculated results using the Baldwin-Lomax (1978) model are in better agreement with the data than the Jones-Launder (1972) model. Within the inner portion of the boundary layer, both models tend to underpredict the yaw angle.

  1. Development and application of a three-dimensional finite element vapor intrusion model.

    PubMed

    Pennell, Kelly G; Bozkurt, Ozgur; Suuberg, Eric M

    2009-04-01

    Details of a three-dimensional finite element model of soil vapor intrusion, including the overall modeling process and the stepwise approach, are provided. The model is a quantitative modeling tool that can help guide vapor intrusion characterization efforts. It solves the soil gas continuity equation coupled with the chemical transport equation, allowing for both advective and diffusive transport. Three-dimensional pressure, velocity, and chemical concentration fields are produced from the model. Results from simulations involving common site features, such as impervious surfaces, porous foundation sub-base material, and adjacent structures are summarized herein. The results suggest that site-specific features are important to consider when characterizing vapor intrusion risks. More importantly, the results suggest that soil gas or subslab gas samples taken without proper regard for particular site features may not be suitable for evaluating vapor intrusion risks; rather, careful attention needs to be given to the many factors that affect chemical transport into and around buildings. PMID:19418819

  2. Three-dimensional Fast Flux Test Facility plenum model turbulent flow prediction and data comparison

    SciTech Connect

    Eyler, L.L.; Sawdye, R.W.

    1981-01-01

    Two- and three-dimensional numerical simulations of turbulent flow in a scaled Fast Flux Test Facility (FFTF) upper plenum model were performed using the TEMPEST hydrothermal code. A standard k-element of model was used to describe turbulence through an effective viscosity. Comparisons with previously reported mean velocity and turbulence field data measured in the plenum model and two-dimensional numerical simulations using the TEACH code were made. Predicted horizontal and vertical mean velocities and turbulent kinetic energy are shown to be in good agreement with available experimental data when inlet conditions of the dissipation of turbulent kinetic energy are appropriately prescribed. The three-dimensional quarter-symmetry simulation predicts the turbulent kinetic energy field significantly better than the two-dimensional centerplane simulations. These results lead to conclusions concerning deficiencies in the experimental data and the turbulence model.

  3. Three-dimensional thermal finite element modeling of lithium-ion battery in thermal abuse application

    NASA Astrophysics Data System (ADS)

    Guo, Guifang; Long, Bo; Cheng, Bo; Zhou, Shiqiong; Xu, Peng; Cao, Binggang

    In order to better understand the thermal abuse behavior of high capacities and large power lithium-ion batteries for electric vehicle application, a three-dimensional thermal model has been developed for analyzing the temperature distribution under abuse conditions. The model takes into account the effects of heat generation, internal conduction and convection, and external heat dissipation to predict the temperature distribution in a battery. Three-dimensional model also considers the geometrical features to simulate oven test, which are significant in larger cells for electric vehicle application. The model predictions are compared to oven test results for VLP 50/62/100S-Fe (3.2 V/55 Ah) LiFePO 4/graphite cells and shown to be in great agreement.

  4. Three-dimensional forecasting models on a desk-top computer

    SciTech Connect

    Yamada, T.; Bunker, S.

    1990-01-01

    Recent advances in the desk-top computer capabilities, particularly those of an engineering workstation, are truly astonishing. A high performance workstation reportedly exceeded a supercomputer in certain scaler operations. Affordability and portability of a desk- top computer opened doors to many applications which were previously considered impossible. The purpose of the present study is to demonstrate the feasibility of using and engineering workstation to operate a three-dimensional mesoscale modeling system to describe the transport and dispersion of atmospheric pollutants over complex terrain surrounding Vandenberg Air Force Base (VAFB), Vandenberg, California. Our modeling system is composed of two numerical codes, HOTMAC, and RAPTAD. HOTMAC is a mesoscale forecast code that is able to model three-dimensional distributions of wind speed, wind direction, turbulence, temperature, and water vapor. RAPTAD is a Lagrangian puff code based on the Monte Carlo statistical diffusion process. RAPTAD can be used under extreme conditions where a conventional Gaussian plume model may fail.

  5. A three-dimensional statistical mechanical model of folding double-stranded chain molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbing; Chen, Shi-Jie

    2001-05-01

    Based on a graphical representation of intrachain contacts, we have developed a new three-dimensional model for the statistical mechanics of double-stranded chain molecules. The theory has been tested and validated for the cubic lattice chain conformations. The statistical mechanical model can be applied to the equilibrium folding thermodynamics of a large class of chain molecules, including protein β-hairpin conformations and RNA secondary structures. The application of a previously developed two-dimensional model to RNA secondary structure folding thermodynamics generally overestimates the breadth of the melting curves [S-J. Chen and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. 97, 646 (2000)], suggesting an underestimation for the sharpness of the conformational transitions. In this work, we show that the new three-dimensional model gives much sharper melting curves than the two-dimensional model. We believe that the new three-dimensional model may give much improved predictions for the thermodynamic properties of RNA conformational changes than the previous two-dimensional model.

  6. Documentation of finite-difference model for simulation of three-dimensional ground-water flow

    USGS Publications Warehouse

    Trescott, Peter C.; Larson, S.P.

    1976-01-01

    User experience has indicated that the documentation of the model of three-dimensional ground-water flow (Trescott and Larson, 1975) should be expanded. This supplement is intended to fulfill that need. The original report emphasized the theory of the strongly implicit procedure, instructions for using the groundwater-flow model, and practical considerations for application. (See also W76-02962 and W76-13085) (Woodard-USGS)

  7. Three-Dimensional In Vitro Tumor Models for Cancer Research and Drug Evaluation

    PubMed Central

    Xu, Xian; Farach-Carson, Mary C.; Jia, Xinqiao

    2014-01-01

    Cancer occurs when cells acquire genomic instability and inflammation, produce abnormal levels of epigenetic factors/proteins and tumor suppressors, reprogram the energy metabolism and evade immune destruction, leading to the disruption of cell cycle/normal growth. An early event in carcinogenesis is loss of polarity and detachment from the natural basement membrane, allowing cells to form distinct three-dimensional (3D) structures that interact with each other and with the surrounding microenvironment. Although valuable information has been accumulated from traditional in vitro studies in which cells are grown on flat and hard plastic surfaces (2D culture), this culture condition does not reflect the essential features of tumor tissues. Further, fundamental understanding of cancer metastasis cannot be obtained readily from 2D studies because they lack the complex and dynamic cell-cell communications and cell-matrix interactions that occur during cancer metastasis. These shortcomings, along with lack of spatial depth and cell connectivity, limit the applicability of 2D cultures to accurate testing of pharmacologically active compounds, free or sequestered in nanoparticles. To recapitulate features of native tumor microenvironments, various biomimetic 3D tumor models have been developed to incorporate cancer and stromal cells, relevant matrix components, and biochemical and biophysical cues, into one spatially and temporally integrated system. In this article, we review recent advances in creating 3D tumor models employing tissue engineering principles. We then evaluate the utilities of these novel models for the testing of anticancer drugs and their delivery systems. We highlight the profound differences in responses from 3D in vitro tumors and conventional monolayer cultures. Overall, strategic integration of biological principles and engineering approaches will both improve understanding of tumor progression and invasion and support discovery of more personalized

  8. Three-dimensional left ventricular segmentation from magnetic resonance imaging for patient-specific modelling purposes

    PubMed Central

    Caiani, Enrico G.; Colombo, Andrea; Pepi, Mauro; Piazzese, Concetta; Maffessanti, Francesco; Lang, Roberto M.; Carminati, Maria Chiara

    2014-01-01

    Aims To propose a nearly automated left ventricular (LV) three-dimensional (3D) surface segmentation procedure, based on active shape modelling (ASM) and built on a database of 3D echocardiographic (3DE) LV surfaces, for cardiac magnetic resonance (CMR) images, and to test its accuracy for LV volumes computation compared with ‘gold standard’ manual tracings and discs-summation method. Methods and results The ASM was created based on segmented LV surfaces (4D LV analysis, Tomtec) from 3DE datasets of 205 patients. Then, it was applied to the cardiac magnetic resonance imaging short-axis (SAX) images stack of 12 consecutive patients. After proper realignment using two- and four-chambers CMR long-axis views both as reference and for initializing LV apex and base (six points in total), the ASM was iteratively and automatically updated to match the information of all the SAX planes contemporaneously, resulting in an endocardial LV 3D mesh from which volume was directly derived. The same CMR images were analysed by an experienced cardiologist to derive end-diastolic and end-systolic volumes. Linear correlation and Bland–Altman analyses were applied vs. the manual ‘gold standard’. Active shape modelling results showed high correlations with manual values both for LV volumes (r2 > 0.98) and ejection fraction (EF) (r2 > 0.90), non-significant biases and narrow limits of agreement. Conclusion The proposed method resulted in accurate detection of 3D LV endocardial surfaces, which lead to fast and reliable measurements of LV volumes and EF when compared with manual tracing of CMR SAX images. The segmented 3D mesh, including a realistic LV apex and base, could constitute a novel starting point for more realistic patient-specific finite element modelling. PMID:25362176

  9. A three-dimensional thermal abuse model for lithium-ion cells

    NASA Astrophysics Data System (ADS)

    Kim, Gi-Heon; Pesaran, Ahmad; Spotnitz, Robert

    To understand further the thermal abuse behavior of large format Li-ion batteries for automotive applications, the one-dimensional modeling approach formulated by Hatchard et al. [T.D. Hatchard, D.D. MacNeil, A. Basu, J.R. Dahn, J. Electrochem. Soc. 148(7) (2001) A755-A761] was reproduced. Then it was extended to three dimensions so we could consider the geometrical features, which are critical in large cells for automotive applications. The three-dimensional model captures the shapes and dimensions of cell components and the spatial distributions of materials and temperatures, and is used to simulate oven tests, and to determine how a local hot spot can propagate through the cell. In simulations of oven abuse testing of cells with cobalt oxide cathode and graphite anode with standard LiPF 6 electrolyte, the three-dimensional model predicts that thermal runaway will occur sooner or later than the lumped model, depending on the size of the cell. The model results showed that smaller cells reject heat faster than larger cells; this may prevent them from going into thermal runaway under identical abuse conditions. In simulations of local hot spots inside a large cylindrical cell, the three-dimensional model predicts that the reactions initially propagate in the azimuthal and longitudinal directions to form a hollow cylinder-shaped reaction zone.

  10. Accuracy of open-source software segmentation and paper-based printed three-dimensional models.

    PubMed

    Szymor, Piotr; Kozakiewicz, Marcin; Olszewski, Raphael

    2016-02-01

    In this study, we aimed to verify the accuracy of models created with the help of open-source Slicer 3.6.3 software (Surgical Planning Lab, Harvard Medical School, Harvard University, Boston, MA, USA) and the Mcor Matrix 300 paper-based 3D printer. Our study focused on the accuracy of recreating the walls of the right orbit of a cadaveric skull. Cone beam computed tomography (CBCT) of the skull was performed (0.25-mm pixel size, 0.5-mm slice thickness). Acquired DICOM data were imported into Slicer 3.6.3 software, where segmentation was performed. A virtual model was created and saved as an .STL file and imported into Netfabb Studio professional 4.9.5 software. Three different virtual models were created by cutting the original file along three different planes (coronal, sagittal, and axial). All models were printed with a Selective Deposition Lamination Technology Matrix 300 3D printer using 80 gsm A4 paper. The models were printed so that their cutting plane was parallel to the paper sheets creating the model. Each model (coronal, sagittal, and axial) consisted of three separate parts (∼200 sheets of paper each) that were glued together to form a final model. The skull and created models were scanned with a three-dimensional (3D) optical scanner (Breuckmann smart SCAN) and were saved as .STL files. Comparisons of the orbital walls of the skull, the virtual model, and each of the three paper models were carried out with GOM Inspect 7.5SR1 software. Deviations measured between the models analysed were presented in the form of a colour-labelled map and covered with an evenly distributed network of points automatically generated by the software. An average of 804.43 ± 19.39 points for each measurement was created. Differences measured in each point were exported as a .csv file. The results were statistically analysed using Statistica 10, with statistical significance set at p < 0.05. The average number of points created on models for each measurement was 804

  11. The correction of the distortion of human face based on three-dimensional modeling methods

    NASA Astrophysics Data System (ADS)

    Ye, Qingmin; Chen, Kuo; Feng, Huajun; Xu, Zhihai; Li, Qi

    2015-08-01

    When the human face is on the edge of field of the camera which has a large view, serious deformation will be captured. To correct the distortion of the human face, we present an approach based on setting up a 3D model. Firstly, we construct 3D target face modeling by using the data and depth information of the standard human face, which is set up by the three-dimensional model with three-dimensional Gaussian function with sectional type. According to the size of the face in the image and the parameters of the camera, we can obtain the information of relative position and depth of the human face. Then by translating the virtual camera axis to the center of the face, we can achieve the goal to correct the distortion of the face based on the theory of three-dimensional imaging. Finally, we have made a lot of experiments, and we study the influence of parameters of the 3D model of human face. The result indicates that the method presented by this paper can play an effective role in correcting the distortion of the face in the edge of the view, and we can get better results if the model appreciates the real human face.

  12. [The potential of three-dimensional tumor models and cell culturing in cancer research and diagnostics].

    PubMed

    Alföldi, Róbert; Szebeni, János Gábor; Puskás, László G

    2015-12-01

    In vitro testing of antitumor agents on human cancer cell lines has become essential in pharmaceutical research and in clinical practice. Although the most widely used technique is the two-dimensional cell growing protocol (in tissue culture plates), the new three-dimensional methods are becoming more and more popular as their structure and complexity is more similar to the microenvironment of the real tumor. The aim of the present study is to describe the most widely used in vitro three-dimensional tumor models and to compare a RAFT(TM) three dimensional in vitro tumor model with the traditional two-dimensional tumor cell cultures. In the study, the viability and the enzyme activity of cultured A549 non-small cell lung cancer (NSCLC) cells under different conditions were compared. The results show that while the number of necrotic cells increased significantly (20-fold; 2D/A549 T75 conventional tissue culture flask 1.6%; 2D/A549-collagen coated T75 tissue culture flask 1.45%, RAFT(TM) 22.11%) during long culturing period in the RAFT(TM) three-dimensional in vitro tumor model, there was no significant difference during the conventional antitumor screening period (3-5 day) compared to the traditional two-dimensional cell cultures. The structure of the tumor cell islets grown with RAFT(TM) is much more complex than that of the traditional two-dimensional cultures. Thus, similarly to the in vivo tumor microenvironment, there is also a collagen matrix in the extracellular space which can have significant effect on the diffusion of the antitumor agents to cells. In conclusion, it can be stated that testing of antitumor agents on tumor cells cultured in three-dimensional systems can be an important complementary method to the traditional two-dimensional in vitro analyses. The results of the new three-dimensional method can be more easily applied in the in vivo analysis and translated into clinical practice. PMID:26665190

  13. Deep magmatic structures of Hawaiian volcanoes, imaged by three-dimensional gravity models

    USGS Publications Warehouse

    Kauahikaua, J.; Hildenbrand, T.; Webring, M.

    2000-01-01

    A simplified three-dimensional model for the island of Hawai'i, based on 3300 gravity measurements, provides new insights on magma pathways within the basaltic volcanoes. Gravity anomalies define dense cumulates and intrusions beneath the summits and known rift zones of every volcano. Linear gravity anomalies project southeast from Kohala and Mauna Kea summits and south from Huala??lai and Mauna Loa; these presumably express dense cores of previously unrecognized rift zones lacking surface expression. The gravity-modeled dense cores probably define tholeiitic shield-stage structures of the older volcanoes that are now veneered by late alkalic lavas. The three-dimensional gravity method is valuable for characterizing the magmatic systems of basaltic oceanic volcanoes and for defining structures related to landslide and seismic hazards.

  14. Nematic order by thermal disorder in a three-dimensional lattice spin model with dipolarlike interactions.

    PubMed

    Chamati, Hassan; Romano, Silvano

    2014-08-01

    At low temperatures, some lattice spin models with simple ferromagnetic or antiferromagnetic interactions (for example, nearest-neighbor interaction being isotropic in spin space on a bipartite three-dimensional lattice) produce orientationally ordered phases exhibiting nematic (second-rank) order, in addition to the primary first-rank one; on the other hand, in the literature, they have been rather seldom investigated in this respect. Here we study the thermodynamic properties of a three-dimensional model with dipolar-like interaction. Its ground state is found to exhibit full orientational order with respect to a suitably defined staggered magnetization (polarization), but no nematic second-rank order. Extensive Monte Carlo simulations, in conjunction with finite-size scaling analysis, have been used for characterizing its critical behavior; on the other hand, it has been found that nematic order does indeed set in at low temperatures, via a mechanism of order by disorder. PMID:25215748

  15. Three-Dimensional Transgenic Cell Models to Quantify Space Genotoxic Effects

    NASA Technical Reports Server (NTRS)

    Gonda, S.; Wu, H.; Pingerelli, P.; Glickman, B.

    2000-01-01

    In this paper we describe a three-dimensional, multicellular tissue-equivalent model, produced in NASA-designed, rotating wall bioreactors using mammalian cells engineered for genomic containment of mUltiple copies of defined target genes for genotoxic assessment. The Rat 2(lambda) fibroblasts (Stratagene, Inc.) were genetically engineered to contain high-density target genes for mutagenesis. Stable three-dimensional, multicellular spheroids were formed when human mammary epithelial cells and Rat 2(lambda) fibroblasts were cocultured on Cytodex 3 Beads in a rotating wall bioreactor. The utility of this spheroidal model for genotoxic assessment was indicated by a linear dose response curve and by results of gene sequence analysis of mutant clones from 400micron diameter spheroids following low-dose, high-energy, neon radiation exposure

  16. Modeling dynamic reciprocity: Engineering three-dimensional culture models of breast architecture, function, and neoplastic transformation

    PubMed Central

    Nelson, Celeste M.; Bissell, Mina J.

    2010-01-01

    In order to understand why cancer develops as well as predict the outcome of pharmacological treatments, we need to model the structure and function of organs in culture so that our experimental manipulations occur under physiological contexts. This review traces the history of the development of a prototypic example, the three-dimensional (3D) model of the mammary gland acinus. We briefly describe the considerable information available on both normal mammary gland function and breast cancer generated by the current model and present future challenges that will require an increase in its complexity. We propose the need for engineered tissues that faithfully recapitulate their native structures to allow a greater understanding of tissue function, dysfunction, and potential therapeutic intervention. PMID:15963732

  17. Liquid-based three-dimensional tumor models for cancer research and drug discovery

    PubMed Central

    Ham, Stephanie L; Joshi, Ramila; Thakuri, Pradip S

    2016-01-01

    Tumors are three-dimensional tissues where close contacts between cancer cells, intercellular interactions between cancer and stromal cells, adhesion of cancer cells to the extracellular matrix, and signaling of soluble factors modulate functions of cancer cells and their response to therapeutics. Three-dimensional cultures of cancer cells overcome limitations of traditionally used monolayer cultures and recreate essential characteristics of tumors such as spatial gradients of oxygen, growth factors, and metabolites and presence of necrotic, hypoxic, quiescent, and proliferative cells. As such, three-dimensional tumor models provide a valuable tool for cancer research and oncology drug discovery. Here, we describe different tumor models and primarily focus on a model known as tumor spheroid. We summarize different technologies of spheroid formation, and discuss the use of spheroids to address the influence of stromal fibroblasts and immune cells on cancer cells in tumor microenvironment, study cancer stem cells, and facilitate compound screening in the drug discovery process. We review major techniques for quantification of cellular responses to drugs and discuss challenges ahead to enable broad utility of tumor spheroids in research laboratories, integrate spheroid models into drug development and discovery pipeline, and use primary tumor cells for drug screening studies to realize personalized cancer treatment. PMID:27072562

  18. Liquid-based three-dimensional tumor models for cancer research and drug discovery.

    PubMed

    Ham, Stephanie L; Joshi, Ramila; Thakuri, Pradip S; Tavana, Hossein

    2016-05-01

    Tumors are three-dimensional tissues where close contacts between cancer cells, intercellular interactions between cancer and stromal cells, adhesion of cancer cells to the extracellular matrix, and signaling of soluble factors modulate functions of cancer cells and their response to therapeutics. Three-dimensional cultures of cancer cells overcome limitations of traditionally used monolayer cultures and recreate essential characteristics of tumors such as spatial gradients of oxygen, growth factors, and metabolites and presence of necrotic, hypoxic, quiescent, and proliferative cells. As such, three-dimensional tumor models provide a valuable tool for cancer research and oncology drug discovery. Here, we describe different tumor models and primarily focus on a model known as tumor spheroid. We summarize different technologies of spheroid formation, and discuss the use of spheroids to address the influence of stromal fibroblasts and immune cells on cancer cells in tumor microenvironment, study cancer stem cells, and facilitate compound screening in the drug discovery process. We review major techniques for quantification of cellular responses to drugs and discuss challenges ahead to enable broad utility of tumor spheroids in research laboratories, integrate spheroid models into drug development and discovery pipeline, and use primary tumor cells for drug screening studies to realize personalized cancer treatment.

  19. GEO3D - Three-Dimensional Computer Model of a Ground Source Heat Pump System

    SciTech Connect

    James Menart

    2013-06-07

    This file is the setup file for the computer program GEO3D. GEO3D is a computer program written by Jim Menart to simulate vertical wells in conjunction with a heat pump for ground source heat pump (GSHP) systems. This is a very detailed three-dimensional computer model. This program produces detailed heat transfer and temperature field information for a vertical GSHP system.

  20. High performance computing for three-dimensional agent-based molecular models.

    PubMed

    Pérez-Rodríguez, G; Pérez-Pérez, M; Fdez-Riverola, F; Lourenço, A

    2016-07-01

    Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool. PMID:27372059

  1. High performance computing for three-dimensional agent-based molecular models.

    PubMed

    Pérez-Rodríguez, G; Pérez-Pérez, M; Fdez-Riverola, F; Lourenço, A

    2016-07-01

    Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool.

  2. Three-dimensional cluster resolution for guiding automatic chemometric model optimization.

    PubMed

    Sinkov, Nikolai A; Harynuk, James J

    2013-01-15

    A three-dimensional extension of a previously developed metric termed cluster resolution is presented. The cluster resolution metric considers confidence ellipses (here three-dimensional confidence ellipsoids) around clusters of points in principal component or latent variable space. Cluster resolution is defined as the maximum confidence limit at which confidence ellipses do not overlap and can serve to guide automated variable selection processes. Previously, this metric has been used to guide variable selection in a two-dimensional projection of data. In this study, the metric is refined to simultaneously consider the shapes of clusters of points in a three-dimensional space. We couple it with selectivity ratio-based variable ranking and a combined backward elimination/forward selection strategy to demonstrate its use for the automated optimization of a six-class PCA model of gasoline by vendor and octane rating. Within-class variability was artificially increased through evaporative weathering and intentional contamination of samples, making the optimization more challenging. Our approach was successful in identifying a small subset of variables (644) from the raw GC-MS chromatographic data which comprised ≈ 2 × 10(6) variables per sample. In the final model there was clear separation between all classes. Computational time for this completely automated variable selection was 36 h; slower than solving the same problem using three two-dimensional projections, but yielding an overall better model. By simultaneously considering three dimensions instead of only two at a time, the resulting overall cluster resolution was improved.

  3. Three-Dimensional Numerical Models of Subduction and Subduction-Induced Mantle Flow

    NASA Astrophysics Data System (ADS)

    Freeman, J.; Stegman, D. R.; Schellart, W. P.; Moresi, L.; May, D. A.; Turnbull, R.

    2004-12-01

    The kinematics of subduction and its influence on mantle convection and plate-scale deformation have been the focus of numerous geodynamic studies [e.g. Garfunkel et al., 1986; Gurnis and Hager, 1988; Zhong and Gurnis, 1995; Christensen, 1996; Olbertz et al., 1997; Conrad and Hager, 1999; Eberle et al., 2002]. Most geodynamic models have considered only two-dimensional aspects of subduction dynamics by incorporating the assumption that subduction zones are infinite in trench-parallel extent. However, natural subduction zones are intrinsically three-dimensional, due in part to their limited lateral extent. Lateral length scales of natural subduction zones vary from only a few hundred kilometres (e.g. the Calabrian, Hellenic and Scotia slabs) to several thousand kilometres (e.g. the Aleutian, Indonesian, Northwest Pacific and South American slabs). Here, we present results from three-dimensional numerical experiments that simulate lithospheric subduction and subduction induced mantle flow for slabs with a varying lateral extent.

  4. Three-dimensional loop quantum gravity: physical scalar product and spin-foam models

    NASA Astrophysics Data System (ADS)

    Noui, Karim; Perez, Alejandro

    2005-05-01

    In this paper, we address the problem of the dynamics in three-dimensional loop quantum gravity with zero cosmological constant. We construct a rigorous definition of Rovelli's generalized projection operator from the kinematical Hilbert space—corresponding to the quantization of the infinite-dimensional kinematical configuration space of the theory—to the physical Hilbert space. In particular, we provide the definition of the physical scalar product which can be represented in terms of a sum over (finite) spin-foam amplitudes. Therefore, we establish a clear-cut connection between the canonical quantization of three-dimensional gravity and spin-foam models. We emphasize two main properties of the result: first that no cut-off in the kinematical degrees of freedom of the theory is introduced (in contrast to standard 'lattice' methods), and second that no ill-defined sum over spins ('bubble' divergences) are present in the spin-foam representation.

  5. Three-dimensional modelling of horizontal chemical vapor deposition. I - MOCVD at atmospheric pressure

    NASA Technical Reports Server (NTRS)

    Ouazzani, Jalil; Rosenberger, Franz

    1990-01-01

    A systematic numerical study of the MOCVD of GaAs from trimethylgallium and arsine in hydrogen or nitrogen carrier gas at atmospheric pressure is reported. Three-dimensional effects are explored for CVD reactors with large and small cross-sectional aspect ratios, and the effects on growth rate uniformity of tilting the susceptor are investigated for various input flow rates. It is found that, for light carrier gases, thermal diffusion must be included in the model. Buoyancy-driven three-dimensional flow effects can greatly influence the growth rate distribution through the reactor. The importance of the proper design of the lateral thermal boundary conditions for obtaining layers of uniform thickness is emphasized.

  6. About Dark Energy and Dark Matter in a Three-Dimensional Quantum Vacuum Model

    NASA Astrophysics Data System (ADS)

    Fiscaletti, Davide

    2016-10-01

    A model of a three-dimensional quantum vacuum based on Planck energy density as a universal property of a granular space is suggested. The possibility to provide an unifying explanation of dark matter and dark energy as phenomena linked with the fluctuations of the three-dimensional quantum vacuum is explored. The changes and fluctuations of the quantum vacuum energy density generate a curvature of space-time similar to the curvature produced by a "dark energy" density. The formation of large scale structures in the universe associated to the flattening of the orbital speeds of the spiral galaxies can be explained in terms of primary fluctuations of the quantum vacuum energy density without attracting the idea of dark matter.

  7. Testing and benchmarking of a three-dimensional groundwater flow and solute transport model

    SciTech Connect

    Sims, P.N.; Andersen, P.F.; Faust, C.R.; Stephenson, D.E.

    1988-12-31

    A three-dimensional finite-difference model was developed to simulate groundwater flow and solute transport. The model is intended for application to a variety of groundwater resource and solute migration evaluations, including several complex sites at the Savannah River Plant (SRP). Because the model, FTWORK, is relatively new, there is a need to provide confidence in the model results. Methodologies that test models include comparisons with analytical solutions, comparisons with empirical data, and checking that conservation properties hold. Another level of testing is the comparison of one code against another. This paper describes the testing and benchmarking procedure used to verify the validate FTWORK.

  8. Dynamics and stability of a three-dimensional model of cell signal transduction with delay

    NASA Astrophysics Data System (ADS)

    Levy, Chris; Iron, David

    2015-07-01

    In this paper, we consider a three-dimensional model of cell signal transduction with delay. The deactivation of signalling proteins occurs throughout the cytosol and activation is localized to specific sites in the cell. The enzyme kinetic functions employ a constant delay to model the time lapse during reactions and also the recovery times associated with conformational changes. We use matched asymptotic expansions to construct the dynamic solutions of signalling protein concentrations. The result of the asymptotic analysis is a system of delayed differential algebraic equations. This reduced system is compared to numerical simulations of the full three-dimensional system. As well, we consider the stability of equilibrium solutions. We find that the systems under consideration may undergo Hopf bifurcations for certain delay values. In these cases sustained oscillations are observed. The Poincaré-Lindstedt3 method is used to improve upon the asymptotic approximations. The simulations of the full three-dimensional system correspond well with simulations of the reduced delayed differential algebraic equations.

  9. Efficient three-dimensional ray-tracing model for electromagnetic propagation prediction in complex indoor environments.

    PubMed

    Liu, Z-Y; Guo, L-X; Meng, X

    2013-08-01

    A three-dimensional ray-tracing model for the use of the uniform theory of diffraction and geometrical optics in radio channel characterizations of indoor environments is presented in this paper. Based on the environment information chosen by the proposed modeling approach, the model is effectively applied by utilizing a technique in which multiple reflections, transmissions, and diffractions are considered via the ray-path classification into four different categories. Ray paths belonging to each ray category are determined by using different methods. Our theoretical results are compared with narrowband and wideband measurements. The good agreement with these measurements indicates that our prediction model works well for such indoor communication applications.

  10. Explorable Three-Dimensional Digital Model of the Female Pelvis, Pelvic Contents, and Perineum for Anatomical Education

    ERIC Educational Resources Information Center

    Sergovich, Aimee; Johnson, Marjorie; Wilson, Timothy D.

    2010-01-01

    The anatomy of the pelvis is complex, multilayered, and its three-dimensional organization is conceptually difficult for students to grasp. The aim of this project was to create an explorable and projectable stereoscopic, three-dimensional (3D) model of the female pelvis and pelvic contents for anatomical education. The model was created using…

  11. Three-dimensional forward modelling and inversion of complex resistivity based on the improved quasi-linear approximation

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Li, T.; Zhu, C.; Zhang, R.; Wu, Y.

    2015-12-01

    Three-dimensional (3-D) electromagnetic (EM) forward modelling and inversion continues to be an important issue for the correct interpretation of EM data.To this end,approximate solutions have been developed that allow the construction of relatively fast forward modelling and inversion schemes.We have developed an improved quasi-linear approximation which is more appropriate in solving the linear equation for greatly shortening calculation time.We achieved this by using green's function properties.Then we introduced the improved quasi-linear approximation to spectral induced polarization (SIP) to tackle the problem of the resolution and the efficiency.The localized quasi-linear (LQL) approximation theory is appropriate for multisource array-type surveys assuming that the normal field is slowly varying within the inhomogeneity domain.However,the normal field of attenuates severely which dose not satisfy the assumption of the LQL approximation.As a consenquence,the imaginary part is not accurate when LQL approximation is adopted for the simulation.The improved quasi-linear approximation provide a new approach with the same resolution of QL approximation and much less calculation time.We have also constructed three-dimensional SIP forward modeling based on improved quasi-linear approximation method.It only takes 0.8s for forward modeling when inhomogeneity domain is divided into 2000 blocks.Beyond that, we have introduced the Cole-Cole model to the algorithm and complete the three-dimensional complex resistivity conjugate gradient inversion with parameter restraint.The model trial results show that this method can obtain good inversion results in physical parameters such as zero frequency resistivity, polarization.The results demonstrate the stability and the efficiency of the improved quasi-linear approximation and the method may be a practical solution for3-D EM forward modelling and inversion of SIP.

  12. Three-Dimensional Computational Model for Flow in an Over-Expanded Nozzle With Porous Surfaces

    NASA Technical Reports Server (NTRS)

    Abdol-Hamid, K. S.; Elmiligui, Alaa; Hunter, Craig A.; Massey, Steven J.

    2006-01-01

    A three-Dimensional computational model is used to simulate flow in a non-axisymmetric, convergent-divergent nozzle incorporating porous cavities for shock-boundary layer interaction control. The nozzle has an expansion ratio (exit area/throat area) of 1.797 and a design nozzle pressure ratio of 8.78. Flow fields for the baseline nozzle (no porosity) and for the nozzle with porous surfaces of 10% openness are computed for Nozzle Pressure Ratio (NPR) varying from 1.29 to 9.54. The three dimensional computational results indicate that baseline (no porosity) nozzle performance is dominated by unstable, shock-induced, boundary-layer separation at over-expanded conditions. For NPR less than or equal to 1.8, the separation is three dimensional, somewhat unsteady, and confined to a bubble (with partial reattachment over the nozzle flap). For NPR greater than or equal to 2.0, separation is steady and fully detached, and becomes more two dimensional as NPR increased. Numerical simulation of porous configurations indicates that a porous patch is capable of controlling off design separation in the nozzle by either alleviating separation or by encouraging stable separation of the exhaust flow. In the present paper, computational simulation results, wall centerline pressure, mach contours, and thrust efficiency ratio are presented, discussed and compared with experimental data. Results indicate that comparisons are in good agreement with experimental data. The three-dimensional simulation improves the comparisons for over-expanded flow conditions as compared with two-dimensional assumptions.

  13. Three-dimensional in vitro cancer spheroid models for Photodynamic Therapy: Strengths and Opportunities

    NASA Astrophysics Data System (ADS)

    Evans, Conor

    2015-03-01

    Three dimensional, in vitro spheroid cultures offer considerable utility for the development and testing of anticancer photodynamic therapy regimens. More complex than monolayer cultures, three-dimensional spheroid systems replicate many of the important cell-cell and cell-matrix interactions that modulate treatment response in vivo. Simple enough to be grown by the thousands and small enough to be optically interrogated, spheroid cultures lend themselves to high-content and high-throughput imaging approaches. These advantages have enabled studies investigating photosensitizer uptake, spatiotemporal patterns of therapeutic response, alterations in oxygen diffusion and consumption during therapy, and the exploration of mechanisms that underlie therapeutic synergy. The use of quantitative imaging methods, in particular, has accelerated the pace of three-dimensional in vitro photodynamic therapy studies, enabling the rapid compilation of multiple treatment response parameters in a single experiment. Improvements in model cultures, the creation of new molecular probes of cell state and function, and innovations in imaging toolkits will be important for the advancement of spheroid culture systems for future photodynamic therapy studies.

  14. Towards three-dimensional continuum models of self-consistent along-strike megathrust segmentation

    NASA Astrophysics Data System (ADS)

    Pranger, Casper; van Dinther, Ylona; May, Dave; Le Pourhiet, Laetitia; Gerya, Taras

    2016-04-01

    into one algorithm. We are working towards presenting the first benchmarked 3D dynamic rupture models as an important step towards seismic cycle modelling of megathrust segmentation in a three-dimensional subduction setting with slow tectonic loading, self consistent fault development, and spontaneous seismicity.

  15. Discovery of novel Myc-Max heterodimer disruptors with a three-dimensional pharmacophore model.

    PubMed

    Mustata, Gabriela; Follis, Ariele Viacava; Hammoudeh, Dalia I; Metallo, Steven J; Wang, Huabo; Prochownik, Edward V; Lazo, John S; Bahar, Ivet

    2009-03-12

    A three-dimensional pharmacophore model was generated utilizing a set of known inhibitors of c-Myc-Max heterodimer formation. The model successfully identified a set of structurally diverse compounds with potential inhibitory activity against c-Myc. Nine compounds were tested in vitro, and four displayed affinities in the micromolar range and growth inhibitory activity against c-Myc-overexpressing cells. These studies demonstrate the applicability of pharmacophore modeling to the identification of novel and potentially more puissant inhibitors of the c-Myc oncoprotein.

  16. A Student-Constructed Three-Dimensional Model of Stars in Nearby Space

    NASA Astrophysics Data System (ADS)

    Furutani, Tracy

    The construction of a three-dimensional model of star distribution within 17 light years of the Sun gives students a hands-on method to understand what might otherwise involve a dry discussion of stellar types and distribution in the Milky Way. The model construction is accompanied by a worksheet that guides students in exploring different information given by the model. Though no assessment of student understanding of stellar distribution or other related topics was done, anecdotal student feedback has been positive, both in the understanding of the material and in the method of delivery.

  17. A three-dimensional tight-binding model for trans-polyacetylene

    SciTech Connect

    Wang, X.; Campbell, D.K.; Lin, H.Q. ); Vogl, P. . Physikdepartment)

    1990-01-01

    We develop a three-dimensional (3-D) generalization of the one-dimensional (1-D), tight-binding Su-Schrieffer-Heeger (SSH) model for trans-(CH){sub x}. Importantly, the model faithfully reflects the 3-D character of the band-edge states as found in ab initio Local-Density-Approximation (LDA) calculations but remains simple enough to be analytically solvable for the dimerized ground state. We examine the density of states and the optical absorption predicted within this model, paying special attention to the roles of the transverse coupling and the polarization of the probing field.

  18. System maintenance manual for master modeling of aerodynamic surfaces by three-dimensional explicit representation

    NASA Technical Reports Server (NTRS)

    Gibson, A. F.

    1983-01-01

    A system of computer programs has been developed to model general three-dimensional surfaces. Surfaces are modeled as sets of parametric bicubic patches. There are also capabilities to transform coordinate to compute mesh/surface intersection normals, and to format input data for a transonic potential flow analysis. A graphical display of surface models and intersection normals is available. There are additional capabilities to regulate point spacing on input curves and to compute surface intersection curves. Internal details of the implementation of this system are explained, and maintenance procedures are specified.

  19. Three-dimensional model for simulating atmospheric dispersion of heavy-gases over complex terrain

    SciTech Connect

    Chan, S.T.

    1997-09-01

    To help understand heavy gas releases and simulate the resultant dispersion, we have developed a three-dimensional finite element model called FEM3 and an improved version names FEM3A for solving the time dependent conservation equations based on generalized anelastic approximation. Recent enhancements to the model to include the treatment of dispersion scenarios involving density variations much larger than the liquefied natural gas range and an advanced turbulence submodel based on the buoyancy-extended transport equations. This paper presents the main features of the present model FEM3C and numerical results from the simulations of a field-scale LNG spill experiment.

  20. Derivation of a three dimensional numerical water quality model for estuary and continental shelf application

    NASA Technical Reports Server (NTRS)

    Spaulding, M.

    1973-01-01

    A derivation is given for a three dimensional mass transport equation which is appropriate for numerical modeling of estuary and continental shelf water quality variations for both the time dependent and steady state cases. A finite difference approximation to the derived equation is presented and a solution scheme for the resulting equations outlined. Preliminary results are obtained using the model for the extremely simple problems which have analytical solutions. The numerical model, as presented, will provide a scheme to study water quality problems in coastal waters for both steady state and time dependent cases.

  1. Coleman-Weinberg mechanism in a three-dimensional supersymmetric Chern-Simons-matter model

    SciTech Connect

    Ferrari, A. F.; Gallegos, E. A.; Gomes, M.; Silva, A. J. da; Lehum, A. C.; Nascimento, J. R.; Petrov, A. Yu.

    2010-07-15

    Using the superfield formalism, we study the dynamical breaking of gauge symmetry and superconformal invariance in the N=1 three-dimensional supersymmetric Chern-Simons model, coupled to a complex scalar superfield with a quartic self-coupling. This is an analogue of the conformally invariant Coleman-Weinberg model in four spacetime dimensions. We show that a mass for the gauge and matter superfields are dynamically generated after two-loop corrections to the effective superpotential. We also discuss the N=2 extension of our work, showing that the Coleman-Weinberg mechanism in such model is not feasible, because it is incompatible with perturbation theory.

  2. Use of three-dimensional medical modeling methods for precise planning of orthognathic surgery.

    PubMed

    Mavili, Mehmet Emin; Canter, Halil Ibrahim; Saglam-Aydinatay, Banu; Kamaci, Soner; Kocadereli, Ilken

    2007-07-01

    Stereolithographic (medical rapid prototyping) biomodeling allows three-dimensional computed tomography to be used to generate solid plastic replicas of anatomic structures. Reports in the literature suggest that such biomodels may have a use in maxillofacial surgery, craniofacial surgery, orthopedics, neurosurgery, otology, vascular, and nasal research. A prospective trial to assess the usefulness of biomodeling in orthognathic surgery has been performed. In 12 patients with mandibular prognathism and/or maxillary retrusion, in addition to routine preoperative cephalometric analysis, preoperative high-resolution (cutting slice thickness of 1 mm) three-dimensional computed tomography scan of the patients was obtained. Raw data obtained from computed tomography scanning was processed with a Mimics 9.22 Software (Materialise's Interactive Medical Image Control System, Belgium). Fabrication of three-dimensional medical models was obtained through a process called powder depositional modeling by use of a Spectrum Z 510 3D Color Printer (Z Corporation, Burlington, MA). Alveolar arches of the maxilla and mandibula of the models were replaced with orthodontic dental cast models. Temporomandibular joints of the models were fixed with Kirschner wire. Maxillary and mandibular bony segments were mobilized according to preoperative orthodontic planning done by analysis of cephalometric plain radiographs. The relation between proximal and distal mandibular segments after bilateral sagittal split osteotomies were evaluated on models preoperatively. The same surgeon had a role in both model cutting preoperatively and as an instructor preoperatively. The same bony relation was observed both in preoperative modelsand in the perioperative surgical field in all patients. Condylar malpositioning was not observed in any of the patients. Studying preoperative planned movements of osteotomized bone segments and observing relations of osteotomized segments of mandibula and maxilla in

  3. Three-dimensional digital holographic aperture synthesis for rapid and highly-accurate large-volume metrology

    NASA Astrophysics Data System (ADS)

    Crouch, Stephen; Kaylor, Brant M.; Barber, Zeb W.; Reibel, Randy R.

    2015-09-01

    Currently large volume, high accuracy three-dimensional (3D) metrology is dominated by laser trackers, which typically utilize a laser scanner and cooperative reflector to estimate points on a given surface. The dependency upon the placement of cooperative targets dramatically inhibits the speed at which metrology can be conducted. To increase speed, laser scanners or structured illumination systems can be used directly on the surface of interest. Both approaches are restricted in their axial and lateral resolution at longer stand-off distances due to the diffraction limit of the optics used. Holographic aperture ladar (HAL) and synthetic aperture ladar (SAL) can enhance the lateral resolution of an imaging system by synthesizing much larger apertures by digitally combining measurements from multiple smaller apertures. Both of these approaches only produce two-dimensional imagery and are therefore not suitable for large volume 3D metrology. We combined the SAL and HAL approaches to create a swept frequency digital holographic 3D imaging system that provides rapid measurement speed for surface coverage with unprecedented axial and lateral resolution at longer standoff ranges. The technique yields a "data cube" of Fourier domain data, which can be processed with a 3D Fourier transform to reveal a 3D estimate of the surface. In this paper, we provide the theoretical background for the technique and show experimental results based on an ultra-wideband frequency modulated continuous wave (FMCW) chirped heterodyne ranging system showing ~100 micron lateral and axial precisions at >2 m standoff distances.

  4. Three-dimensional modeling of supine human and transport system under whole-body vibration.

    PubMed

    Wang, Yang; Rahmatalla, Salam

    2013-06-01

    The development of predictive computer human models in whole-body vibration has shown some success in predicting simple types of motion, mostly for seated positions and in the uniaxial vertical direction. The literature revealed only a handful of papers that tackled supine human modeling in response to vertical vibration. The objective of this work is to develop a predictive, multibody, three-dimensional human model to simulate the supine human and underlying transport system in response to multidirectional whole-body vibration. A three-dimensional dynamic model of a supine human and its underlying transport system is presented in this work to predict supine-human biodynamic response under three-dimensional input random whole-body vibration. The proposed supine-human model consists of three interconnected segments representing the head, torso-arms, and pelvis-legs. The segments are connected via rotational and translational joints that have spring-damper components simulating the three-dimensional muscles and tissuelike connecting elements in the three x, y, and z directions. Two types of transport systems are considered in this work, a rigid support and a long spinal board attached to a standard military litter. The contact surfaces between the supine human and the underlying transport system are modeled using spring-damper components. Eight healthy supine human subjects were tested under combined-axis vibration files with a magnitude of 0.5 m/s2 (rms) and a frequency content of 0.5-16 Hz. The data from seven subjects were used in parameter identification for the dynamic model using optimization schemes in the frequency domain that minimize the differences between the magnitude and phase of the predicted and experimental transmissibility. The predicted accelerations in the time and frequency domains were comparable to those gathered from experiments under different anthropometric, input vibration, and transport conditions under investigation. Based on the

  5. Development of Holistic Three-Dimensional Models for Cold Spray Supersonic Jet

    NASA Astrophysics Data System (ADS)

    Zahiri, S. H.; Phan, T. D.; Masood, S. H.; Jahedi, M.

    2014-08-01

    A three-dimensional, computational fluid dynamics (CFD) model is developed to estimate cold spray gas conditions. This model is calibrated and validated with respect to thermal history of a substrate exposed to the cold spray supersonic jet. The proposed holistic model is important to track state of gas and particles from injection point to the substrate surface with significant benefits for optimization of very rapid "nanoseconds" cold spray deposition. The three-dimensional model is developed with careful attention with respect to computation time to benefit broader cold spray industry with limited access to supercomputers. The k-ɛ-type CFD model is evaluated using measured temperature for a titanium substrate exposed to cold spray nitrogen at 800 °C and 3 MPa. The model important parameters are detailed including domain meshing method with turbulence, and dissipation coefficients during spraying. Heat transfer and radiation are considered for the de Laval nozzle used in experiments. The calibrated holistic model successfully estimated state of the gas for chosen high temperature and high pressure cold spray parameters used in this study. Further to this, the holistic model predictions with respect to the substrate maximum temperature had a good agreement with earlier findings in the literature.

  6. Use of a Three Dimensional Printed Cardiac Model to Assess Suitability for Biventricular Repair.

    PubMed

    Farooqi, Kanwal M; Gonzalez-Lengua, Carlos; Shenoy, Rajesh; Sanz, Javier; Nguyen, Khanh

    2016-05-01

    Three dimensional (3D) printing is rapidly gaining interest in the medical field for use in presurgical planning. We present the case of a seven-year-old boy with double outlet right ventricle who underwent a bidirectional Glenn anastomosis. We used a 3D cardiac model to assess his suitability for a biventricular repair. He underwent a left ventricle-to-aorta baffle with a right ventricle-to-pulmonary artery conduit placement. He did well postoperatively and was discharged home with no evidence of baffle obstruction and good biventricular function. A 3D printed model can provide invaluable intracardiac spatial information in these complex patients.

  7. Three-Dimensional Model for Preservation and Restoration of Architectural Heritage

    NASA Technical Reports Server (NTRS)

    Marchis, Elena

    2011-01-01

    Thc aim of the research will be to create a model, three-dimensional mathematical. implementation. consultation and assistance to "large" restoration projects that will assist the structural analysis, allowing easier display of dynamic strain. analysis and lighting noise. It could also be a valuable tool for decision support. therefore. may simulate several possible scenarios for intervention, This model appears therefore an excellent support for recovering. ordering and monitoring information about materials and data (stage of restoration. photographs. sampling points. results of diagnostic tests, etc.) collected dynamically during the "life" of the cultural heritage. allowing to document its complete history

  8. Three-dimensional interactive graphics for displaying and modelling microscopic data.

    PubMed

    Basinski, M; Deatherage, J F

    1990-09-01

    EUCLID is a three-dimensional (3D) general purpose graphics display package for interactive manipulation of vector, surface and solid drawings on Evans and Sutherland PS300 series graphics processors. It is useful for displaying, comparing, measuring and modelling 3D microscopic images in real time. EUCLID can assemble groups of drawings into a composite drawing, while retaining the ability to operate upon the individual drawings within the composite drawing separately. EUCLID is capable of real time geometrical transformations (scaling, translation and rotation in two coordinate frames) and stereo and perspective viewing transformations. Because of its flexibility, EUCLID is especially useful for fitting models into 3D microscopic images.

  9. Prediction of the three-dimensional structure of human interleukin-7 by homology modeling.

    PubMed

    Kroemer, R T; Doughty, S W; Robinson, A J; Richards, W G

    1996-06-01

    The three-dimensional structure of human interleukin (IL)-7 has been predicted based on homology to human IL-2, IL-4, granulocyte-macrophage colony stimulating factor and growth hormone. The model has a topology common to other cytokines and displays a unique disulfide pattern. Knowledge of the tertiary structure of IL-7 has implications for analysis of key binding regions, suggestions for mutagenesis experiments and design of (ant)agonists. In this context, the model is discussed and compared with other cytokine structures. PMID:8862549

  10. A numerical code for a three-dimensional magnetospheric MHD equilibrium model

    NASA Technical Reports Server (NTRS)

    Voigt, G.-H.

    1992-01-01

    Two dimensional and three dimensional MHD equilibrium models were begun for Earth's magnetosphere. The original proposal was motivated by realizing that global, purely data based models of Earth's magnetosphere are inadequate for studying the underlying plasma physical principles according to which the magnetosphere evolves on the quasi-static convection time scale. Complex numerical grid generation schemes were established for a 3-D Poisson solver, and a robust Grad-Shafranov solver was coded for high beta MHD equilibria. Thus, the effects were calculated of both the magnetopause geometry and boundary conditions on the magnetotail current distribution.

  11. Use of a Three Dimensional Printed Cardiac Model to Assess Suitability for Biventricular Repair.

    PubMed

    Farooqi, Kanwal M; Gonzalez-Lengua, Carlos; Shenoy, Rajesh; Sanz, Javier; Nguyen, Khanh

    2016-05-01

    Three dimensional (3D) printing is rapidly gaining interest in the medical field for use in presurgical planning. We present the case of a seven-year-old boy with double outlet right ventricle who underwent a bidirectional Glenn anastomosis. We used a 3D cardiac model to assess his suitability for a biventricular repair. He underwent a left ventricle-to-aorta baffle with a right ventricle-to-pulmonary artery conduit placement. He did well postoperatively and was discharged home with no evidence of baffle obstruction and good biventricular function. A 3D printed model can provide invaluable intracardiac spatial information in these complex patients. PMID:27009890

  12. Heterogeneous three-dimensional anatomical and electrophysiological model of human atria.

    PubMed

    Seemann, Gunnar; Höper, Christine; Sachse, Frank B; Dössel, Olaf; Holden, Arun V; Zhang, Henggui

    2006-06-15

    Investigating the mechanisms underlying the genesis and conduction of electrical excitation in the atria at physiological and pathological states is of great importance. To provide knowledge concerning the mechanisms of excitation, we constructed a biophysical detailed and anatomically accurate computer model of human atria that incorporates both structural and electrophysiological heterogeneities. The three-dimensional geometry was extracted from the visible female dataset. The sinoatrial node (SAN) and atrium, including crista terminalis (CT), pectinate muscles (PM), appendages (APG) and Bachmann's bundle (BB) were segmented in this work. Fibre orientation in CT, PM and BB was set to local longitudinal direction. Descriptions for all used cell types were based on modifications of the Courtemanche et al. model of a human atrial cell. Maximum conductances of Ito, IKr and ICa,L were modified for PM, CT, APG and atrioventricular ring to reproduce measured action potentials (AP). Pacemaker activity in the human SAN was reproduced by removing IK1, but including If, ICa,T, and gradients of channel conductances as described in previous studies for heterogeneous rabbit SAN. Anisotropic conduction was computed with a monodomain model using the finite element method. The transversal to longitudinal ratio of conductivity for PM, CT and BB was 1:9. Atrial working myocardium (AWM) was set to be isotropic. Simulation of atrial electrophysiology showed initiation of APs in the SAN centre. The excitation spread afterwards to the periphery near to the region of the CT and preferentially towards the atrioventricular region. The excitation extends over the right atrium along PM. Both CT and PM activated the right AWM. Earliest activation of the left atrium was through BB and excitation spread over to the APG. The conduction velocities were 0.6ms-1 for AWM, 1.2ms-1 for CT, 1.6ms-1 for PM and 1.1ms-1 for BB at a rate of 63bpm. The simulations revealed that bundles form dominant

  13. Three-Dimensional, Transgenic Cell Models to Quantify Space Genotoxic Effects

    NASA Technical Reports Server (NTRS)

    Gonda, S. R.; Sognier, M. A.; Wu, H.; Pingerelli, P. L.; Glickman, B. W.; Dawson, David L. (Technical Monitor)

    1999-01-01

    The space environment contains radiation and chemical agents known to be mutagenic and carcinogenic to humans. Additionally, microgravity is a complicating factor that may modify or synergize induced genotoxic effects. Most in vitro models fail to use human cells (making risk extrapolation to humans more difficult), overlook the dynamic effect of tissue intercellular interactions on genotoxic damage, and lack the sensitivity required to measure low-dose effects. Currently a need exists for a model test system that simulates cellular interactions present in tissue, and can be used to quantify genotoxic damage induced by low levels of radiation and chemicals, and extrapolate assessed risk to humans. A state-of-the-art, three-dimensional, multicellular tissue equivalent cell culture model will be presented. It consists of mammalian cells genetically engineered to contain multiple copies of defined target genes for genotoxic assessment,. NASA-designed bioreactors were used to coculture mammalian cells into spheroids, The cells used were human mammary epithelial cells (H184135) and Stratagene's (Austin, Texas) Big Blue(TM) Rat 2 lambda fibroblasts. The fibroblasts were genetically engineered to contain -a high-density target gene for mutagenesis (60 copies of lacl/LacZ per cell). Tissue equivalent spheroids were routinely produced by inoculation of 2 to 7 X 10(exp 5) fibroblasts with Cytodex 3 beads (150 micrometers in diameter). at a 20:1 cell:bead ratio, into 50-ml HARV bioreactors (Synthecon, Inc.). Fibroblasts were cultured for 5 days, an equivalent number of epithelial cells added, and the fibroblast/epithelial cell coculture continued for 21 days. Three-dimensional spheroids with diameters ranging from 400 to 600 micrometers were obtained. Histological and immunohistochemical Characterization revealed i) both cell types present in the spheroids, with fibroblasts located primarily in the center, surrounded by epithelial cells; ii) synthesis of extracellular matrix

  14. A three-dimensional model of fungal morphogenesis based on the vesicle supply center concept.

    PubMed

    Gierz, G; Bartnicki-Garcia, S

    2001-01-21

    We developed a three-dimensional model of hyphal morphogenesis under the same basic assumption used for the construction of a two-dimensional model. Namely, that the polarized growth of tubular cells (hyphoids) arises from a gradient of wall-building vesicles generated by a vesicle supply center (VSC). Contrary to the 2-D mathematical formulation, the three-dimensional derivation led to an indetermination whose solution required defining a priori the pattern of expansion of the wall, i.e. defining the overall spatial movement of the wall as the newly inserted wall elements displace the existing wall fabric. The patterns of wall expansion can be described by tracing the movement of marker points on the cell surface (point trajectories). Point trajectories were computed for three different modes of wall expansion of the VSC-generated hyphoids: orthogonal, isometric, and rotational. The 3-D VSC models allowed us to either stipulate or calculate the degree of anisotropy for each type of wall expansion. Wireframe models were built to visualize growth anisotropy in each model. Although the overall shape of the three hyphoid models is similar, they differ substantially in point trajectories and anisotropy. Point trajectories are experimentally testable and were the basis for the conclusion that hyphae grow in orthogonal fashion. (Bartnicki-Garcia et al., 2000. Biophys. J.79, 2382-2390.)

  15. Three-dimensional gravity modeling of the geologic structure of Long Valley caldera

    SciTech Connect

    Carle, S.F.

    1988-11-10

    A 48-mGal gravity low coincides with Long Valley caldera and is mainly attributed to low-density caldera fill. Gravity measurements by Unocal Geothermal have been integrated with U.S. Geological Survey data, vastly improving gravity station coverage throughout the caldera. A strong regional gravity trend is mainly attributed to isostasy. A ''best fitting'' (based on regional control of basement densities) Airy-Heiskanen isostatic model was used for the regional correction. A three-dimensional, multiple-unit gravity modeling program with iterative capabilities was developed to model the residual gravity. The density structure of Long Valley caldera and vicinity was modeled with 22 discrete density units, most of which were based on geologic units. Information from drill hole lithologies, surface geology, and structural geology interpretations constrain the model. Some important points revealed by the three-dimensional gravity modeling are that (1) the volume of ejected magma associated with the Bishop Tuff eruption is greater than previously thought, (2) the caldera structure is strongly influenced by precaldera topography and the extensions of major, active faults, (3) the main west ring fracture is coincident with the Inyo Domes--Mono Craters fracture system, (4) a relatively low-density region probably underlies the caldera, and (5) a silicic magma chamber may underlie Devils Postpile. copyright American Geophysical Union 1988

  16. Numerical Simulation on Hydromechanical Coupling in Porous Media Adopting Three-Dimensional Pore-Scale Model

    PubMed Central

    Liu, Jianjun; Song, Rui; Cui, Mengmeng

    2014-01-01

    A novel approach of simulating hydromechanical coupling in pore-scale models of porous media is presented in this paper. Parameters of the sandstone samples, such as the stress-strain curve, Poisson's ratio, and permeability under different pore pressure and confining pressure, are tested in laboratory scale. The micro-CT scanner is employed to scan the samples for three-dimensional images, as input to construct the model. Accordingly, four physical models possessing the same pore and rock matrix characteristics as the natural sandstones are developed. Based on the micro-CT images, the three-dimensional finite element models of both rock matrix and pore space are established by MIMICS and ICEM software platform. Navier-Stokes equation and elastic constitutive equation are used as the mathematical model for simulation. A hydromechanical coupling analysis in pore-scale finite element model of porous media is simulated by ANSYS and CFX software. Hereby, permeability of sandstone samples under different pore pressure and confining pressure has been predicted. The simulation results agree well with the benchmark data. Through reproducing its stress state underground, the prediction accuracy of the porous rock permeability in pore-scale simulation is promoted. Consequently, the effects of pore pressure and confining pressure on permeability are revealed from the microscopic view. PMID:24955384

  17. Comprehensive, three-dimensional head-neck model for impact and high-acceleration studies.

    PubMed

    Huston, R L; Huston, J C; Harlow, M W

    1978-01-01

    A three-dimensional, 54-degree-of-freedom computer model of the head/neck system is presented and discussed. The model consists of nine rigid bodies representing the head and vertebrae together with a series of nonlinear springs and dampers modelling the soft tissue. The soft tissue modelling involves the discs, muscles, and ligaments. The discs are modelled as two-parameter viscoelastic solids; the muscles are also modelled as two-parameter viscoelastic solids, but only able to exert force in tension; and the ligaments are modelled as nonlinear elastic bands exerting force only in tension. Equations of motion are written for this model by using Lagrange's form of d'Alembert's principle, a virtual work type principle. Computer algorithms are written to efficiently compute the numerical coefficients of these equations. The equations are integrated numerically for a number of specific cases where experimental data are available. Results show excellent agreement between the model and the experiments.

  18. Semi-Empirical Modeling of Two-Dimensional and Three-Dimensional Dynamic Stall

    NASA Astrophysics Data System (ADS)

    Modarres, Ramin

    Helicopters are generally limited in their performance by the phenomenon of dynamic stall. The purpose of this work is to develop a method for modeling dynamic stall that is appropriate to preliminary design and flight simulator applications. Unlike other semi-empirical dynamic stall models, the model developed in this thesis, not only counts for the well-known, three-dimensional flow effects on the stalled loads but also captures the secondary vortex-shedding phenomenon that has been seen in experiments. The fundamental physics that modify dynamic-stall behavior and that have been extended from two-dimensional to three-dimensional flow are, namely: 1.) yawed flow, 2.) time-varying velocity, 3.) the rotational environment and 4.) the radial blade coupling. For the reduced-order modeling, extra nonlinear states have been added to the dynamic stall model in order to simulate the double-dynamic-stall phenomenon. The results of this study will have practical applications to aerospace systems, such as compliant or morphing surfaces in rotary-wing systems that encounter transient or periodic separation and reattachment during phenomena such as dynamic stall.

  19. Three-Dimensional Numerical Modeling of Initial Mixing of Thermal Discharges at Real-Life Configurations

    SciTech Connect

    Tang, Hansong; Paik, Joongcheol; Sotiropoulos, Fotis; Khangaonkar, Tarang P.

    2008-09-01

    A three-dimensional Reynolds-averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) model is developed for simulating turbulent mixing in the near-field of thermal discharge at real-life geometrical configurations. The domain decomposition method with the multi-level embedded overset grids is employed to handle the complexity of real-life diffusers as well as to efficiently account for the large disparity of length scales arising from the relative size of the ambient river reach and the typical diffuser diameter.

  20. Three-dimensional vector modeling and restoration of flat finite wave tank radiometric measurements

    NASA Technical Reports Server (NTRS)

    Truman, W. M.; Balanis, C. A.

    1977-01-01

    The three-dimensional vector interaction between a microwave radiometer and a wave tank was modeled. Computer programs for predicting the response of the radiometer to the brightness temperature characteristics of the surroundings were developed along with a computer program that can invert (restore) the radiometer measurements. It is shown that the computer programs can be used to simulate the viewing of large bodies of water, and is applicable to radiometer measurements received from satellites monitoring the ocean. The water temperature, salinity, and wind speed can be determined.

  1. Interactive computer graphic surface modeling of three-dimensional solid domains for boundary element analysis

    NASA Technical Reports Server (NTRS)

    Perucchio, R.; Ingraffea, A. R.

    1984-01-01

    The establishment of the boundary element method (BEM) as a valid tool for solving problems in structural mechanics and in other fields of applied physics is discussed. The development of an integrated interactive computer graphic system for the application of the BEM to three dimensional problems in elastostatics is described. The integration of interactive computer graphic techniques and the BEM takes place at the preprocessing and postprocessing stages of the analysis process, when, respectively, the data base is generated and the results are interpreted. The interactive computer graphic modeling techniques used for generating and discretizing the boundary surfaces of a solid domain are outlined.

  2. High resolution measured and modelled three-dimensional airflow over a coastal bowl blowout

    NASA Astrophysics Data System (ADS)

    Smyth, Thomas A. G.; Jackson, Derek W. T.; Cooper, J. Andrew G.

    2012-12-01

    Blowouts are common landforms found within coastal dunes. Their dynamics are primarily driven by aeolian transport caused by surface wind stress, though patterns of deflation and deposition within blowouts are poorly understood as near surface wind flow is complex. Three-dimensional wind flows around blowouts have yet to be properly quantified, especially within zones of separation, re-attachment and acceleration. This has been largely due to inadequate measurement of airflow and a lack of suitable airflow models. With this in mind, we present results from a study that has quantified alongshore and oblique onshore wind flow dynamics over a bowl blowout on the Belmullet Peninsula, Ireland. Using ultrasonic three-dimensional anemometry (measuring at 50 Hz) and three-dimensional computational fluid dynamic (CFD) modelling, we measure and model for the first time in 3D a detailed picture of the heterogeneity of wind flow over this type of terrain. During alongshore wind conditions, wind speeds within the deflation basin were retarded by 50% compared to the foredune zone and flow separation restricted to a small zone in lee of the windward rim. Wind was directed into the deflation basin through a gap in a western erosional wall, termed the blowout throat. In oblique onshore wind, airflow orientated with the blowout throat remained unchanged in direction and slowed by only 30% compared to wind speed on the foredune. In lee of the erosional wall adjacent to the blowout throat, small zones of flow separation occurred close to the erosional wall. In both cases, the highest variation in wind speed and direction occurred in zones of separation and attachment whilst flow increased in steadiness with height over the erosional walls. The results illustrate that wind is manipulated according to localised topography within the bowl blowout itself. Resulting zones of potential sediment transport (erosion and deposition) are spatially complex and alter with wind direction. The

  3. Measurement of three-dimensional stress field of RP model having a notch by using digital holography

    NASA Astrophysics Data System (ADS)

    Tanak, Y.; Murata, S.

    2010-06-01

    We measure three-dimensional stress field of RP model having a V-notch. RP model (Elastic modulues E = 3317 MPa, 9.3 × 7.7 × 50 mm3 having a V-notch) is made of acrylic transparent resin and tracer particle (averaged diameter: 60μm) are dispersed. The model is subjected to the static load (100 N) at the middle. Firstly, three-dimensional deflection is measured by using digital holographic PTV (Particle Tracking Velocimetry). Finally, three-dimensional stress field of RP model is visualized as a differential value of the deflection field.

  4. Three-dimensional compressible jet-in-crossflow calculations using improved viscosity models and adapted grid

    NASA Technical Reports Server (NTRS)

    Lytle, John K.; Harloff, Gary J.; Hsu, Andrew T.

    1990-01-01

    Previous calculations of jet-in-crossflow problems have been sensitive to the turbulence and artificial viscosity models and to the grid. Consequently, the eddy viscosity model in the PARC3D code was modified to consider the turbulent jet by switching from the Baldwin-Lomax (1978) model to an axisymmetric jet model. A modified artificial viscosity model has been utilized and evaluated in this study as well. The new model includes cell size scaling and a directional dependence in the coefficients. Computational results from PARC3D demonstrate the effects of the viscosity models on the pressure distribution fore and aft of the jet and the ability of the adaptive grid scheme to adjust to the three-dimensional gradients around the jet.

  5. Three dimensional electromechanical model of porcine heart with penetrating wound injury.

    PubMed

    Usyk, Taras; Kerckhoffs, Roy

    2005-01-01

    The aim of this study is development a prototype computational model of the pig heart that can be used to predict physiological responses to a penetrating wound injury. The pig has been chosen for this model studies because it shares many anatomical similarities with humans. Three-dimensional cubic Hermite finite element meshes based on detailed measurements of porcine anatomy combined into an integrated anatomic model. The pig ventricular model includes detailed left and right ventricular geometry and myofiber and laminar sheet orientations throughout the mesh. The cardiac mesh was refined and monodomain equations for action potential propagation solved using well-established collocation-Galerkin finite element methods. The membrane kinetic equations for the action potential model was based on detailed cellular models of transmembrane ionic fluxes and intracellular calcium fluxes in canine ventricular myocytes and human atrial myocytes. We modified the anisotropic myocardial conductivity tensor on the endocardial surface of the ventricles by making use of a surface model fitted to measured of Purkinje fiber network anatomy. The mechanical model compute regional three-dimensional stress and strain distributions using anisotropic constitutive laws referred to local material coordinate axes defined by local myofiber and laminar sheet orientations. Passive myocardial mechanics modeled using exponential orthotropic strain energy functions. Active systolic myocardial stresses computed from a multi-scale model that uses crossbridge theory to predict calcium-activated sarcomere length- and velocity-dependent tension filament tension. Since the electrical and mechanical models use a common finite element mesh as the parent parametric framework and both models are solved within our custom finite element package, it is straightforward to couple these models, as we have recently done for a model of coupled ventricular electromechanics. We apply the coupled electromechanical

  6. Three-dimensional lithostratigraphic model at Yucca Mountain, Nevada: A framework for fluid transport modeling and engineering design

    SciTech Connect

    Buesch, D.C.; Spengler, R.W.; Nelson, J.E.; Dickerson, R.P.

    1993-12-31

    A three-dimensional lithostratigraphic model of the central block of Yucca MounEain. Nevada, illustrates how some activities can serve both site characterization and dcsign and construction of the Exploratory Studies Facility (ESF). Site-characterization activities supported bv this model include characterizing the three-dimensional geometry of lithologic units and faults, and providing boundary conditions for geostatistical models and site-scale fluid flow modeling. The model supports the conceptual design as construction efforts for the proposed ramps of the ESF and potential high-level nuclear waste repository.

  7. Experimental validation of a three-dimensional reduced-order continuum model of phonation.

    PubMed

    Farahani, Mehrdad H; Zhang, Zhaoyan

    2016-08-01

    Due to the complex nature of the phonation process, a one-dimensional (1D) glottal flow description is often used in current phonation models. Although widely used in voice research, these 1D flow-based phonation models have not been rigorously validated against experiments. In this study, a 1D glottal flow model is coupled with a three-dimensional nonlinear continuum model of the vocal fold and its predictions are compared to physical model experiments. The results show that the 1D flow-based model is able to predict the phonation threshold pressure and onset frequency within reasonable accuracy and to reproduce major vibratory features observed in the experiments. PMID:27586776

  8. Comparison of three-dimensional parameters of Halo CMEs using three cone models

    NASA Astrophysics Data System (ADS)

    Na, H.; Moon, Y.; Jang, S.; Lee, K.

    2012-12-01

    Halo coronal mass ejections (HCMEs) are a major cause of geomagnetic storms and their three dimensional structures are important for space weather. In this study, we compare three cone models: an elliptical cone model, an ice-cream cone model, and an asymmetric cone model. These models allow us to determine the three dimensional parameters of HCMEs such as radial speed, angular width, and the angle (γ) between sky plane and cone axis. We compare these parameters obtained from three models using 62 well-observed HCMEs observed by SOHO/LASCO from 2001 to 2002. Then we obtain the root mean square error (RMS error) between maximum measured projection speeds and their calculated projection speeds from the cone models. As a result, we find that the radial speeds obtained from the models are well correlated with one another (R > 0.84). The correlation coefficients between angular widths are ranges from 0.04 to 0.53 and those between γ values are from -0.15 to 0.47, which are much smaller than expected. The reason may be due to different assumptions and methods. The RMS errors between the maximum measured projection speeds and the maximum estimated projection speeds of the elliptical cone model, the ice-cream cone model, and the asymmetric cone model are 213 km/s, 254 km/s, and 267 km/s, respectively. And we obtain the correlation coefficients between the location from the models and the flare location (R > 0.75). Finally, we discuss strengths and weaknesses of these models in terms of space weather application.

  9. A three-dimensional meso-macroscopic model for Li-Ion intercalation batteries

    DOE PAGES

    Allu, S.; Kalnaus, S.; Simunovic, S.; Nanda, J.; Turner, J. A.; Pannala, S.

    2016-06-09

    Through this study, we present a three-dimensional computational formulation for electrode-electrolyte-electrode system of Li-Ion batteries. The physical consistency between electrical, thermal and chemical equations is enforced at each time increment by driving the residual of the resulting coupled system of nonlinear equations to zero. The formulation utilizes a rigorous volume averaging approach typical of multiphase formulations used in other fields and recently extended to modeling of supercapacitors [1]. Unlike existing battery modeling methods which use segregated solution of conservation equations and idealized geometries, our unified approach can model arbitrary battery and electrode configurations. The consistency of multi-physics solution also allowsmore » for consideration of a wide array of initial conditions and load cases. The formulation accounts for spatio-temporal variations of material and state properties such as electrode/void volume fractions and anisotropic conductivities. The governing differential equations are discretized using the finite element method and solved using a nonlinearly consistent approach that provides robust stability and convergence. The new formulation was validated for standard Li-ion cells and compared against experiments. Finally, its scope and ability to capture spatio-temporal variations of potential and lithium distribution is demonstrated on a prototypical three-dimensional electrode problem.« less

  10. THREE-DIMENSIONAL IGNITION AND GROWTH REACTIVE FLOW MODELING OF PRISM FAILURE TESTS ON PBX 9502

    SciTech Connect

    Garcia, M L; Tarver, C M

    2006-06-20

    The Ignition and Growth reactive flow model for shock initiation and detonation of solid explosives based on triaminotirnitrobenzene (TATB) is applied to three-dimensional detonation wave propagation. The most comprehensive set of three-dimensional detonation wave propagation data is that measured using the trapezoidal prism test. In this test, a PBX 9501 (95% HMX, 2.5% Estane, and 2.5% BDNPA/F) line detonator initiates a detonation wave along the trapezoidal face of a PBX 9502 (95% TATB and 5% Kel-F binder) prism. The failure thickness, which has been shown experimentally to be roughly half of the failure diameter of a long cylindrical charge, is measured after 50 mm of detonation wave propagation by impact with an aluminum witness plate. The effects of confinement impedance on the PBX 9502 failure thickness have been measured using air (unconfined), water, PMMA, magnesium, aluminum, lead, and copper placed in contact with the rectangular faces of the prism parallel to the direction of detonation propagation. These prism test results are modeled using the two-dimensional PBX 9502 Ignition and Growth model parameters determined by calculating failure diameter and tested on recent corner turning experiments. Good agreement between experimentally measured and calculated prism failure thicknesses for unconfined and confined PBX 9502 is reported.

  11. A three-dimensional meso-macroscopic model for Li-Ion intercalation batteries

    NASA Astrophysics Data System (ADS)

    Allu, S.; Kalnaus, S.; Simunovic, S.; Nanda, J.; Turner, J. A.; Pannala, S.

    2016-09-01

    In this paper we present a three-dimensional computational formulation for electrode-electrolyte-electrode system of Li-Ion batteries. The physical consistency between electrical, thermal and chemical equations is enforced at each time increment by driving the residual of the resulting coupled system of nonlinear equations to zero. The formulation utilizes a rigorous volume averaging approach typical of multiphase formulations used in other fields and recently extended to modeling of supercapacitors [1]. Unlike existing battery modeling methods which use segregated solution of conservation equations and idealized geometries, our unified approach can model arbitrary battery and electrode configurations. The consistency of multi-physics solution also allows for consideration of a wide array of initial conditions and load cases. The formulation accounts for spatio-temporal variations of material and state properties such as electrode/void volume fractions and anisotropic conductivities. The governing differential equations are discretized using the finite element method and solved using a nonlinearly consistent approach that provides robust stability and convergence. The new formulation was validated for standard Li-ion cells and compared against experiments. Its scope and ability to capture spatio-temporal variations of potential and lithium distribution is demonstrated on a prototypical three-dimensional electrode problem.

  12. Investigating the Three-dimensional Flow Separation Induced by a Model Vocal Fold Polyp

    PubMed Central

    Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.

    2014-01-01

    The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. Our laboratory has reported particle image velocimetry (PIV) measurements, within an investigation of a model polyp located on the medial surface of an in vitro driven vocal fold model, which show that such a geometric abnormality considerably disrupts the glottal jet behavior. This flow field adjustment is a likely reason for the severe degradation of the vocal quality in patients with polyps. A more complete understanding of the formation and propagation of vortical structures from a geometric protuberance, such as a vocal fold polyp, and the resulting influence on the aerodynamic loadings that drive the vocal fold dynamics, is necessary for advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp, using an oil-film visualization technique. Unsteady, three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. PMID:24513707

  13. Characterizing natural hydrogel for reconstruction of three-dimensional lymphoid stromal network to model T-cell interactions.

    PubMed

    Kim, Jiwon; Wu, Biming; Niedzielski, Steven M; Hill, Matthew T; Coleman, Rhima M; Ono, Akira; Shikanov, Ariella

    2015-08-01

    Hydrogels have been used in regenerative medicine because they provide a three-dimensional environment similar to soft tissues, allow diffusion of nutrients, present critical biological signals, and degrade via endogenous enzymatic mechanisms. Herein, we developed in vitro system mimicking cell-cell and cell-matrix interactions in secondary lymphoid organs (SLOs). Existing in vitro culture systems cannot accurately represent the complex interactions happening between T-cells and stromal cells in immune response. To model T-cell interaction in SLOs in vitro, we encapsulated stromal cells in fibrin, collagen, or fibrin-collagen hydrogels and studied how different mechanical and biological properties affect stromal network formation. Overall, fibrin supplemented with aprotinin was superior to collagen and fibrin-collagen in terms of network formation and promotion of T-cell penetration. After 8 days of culture, stromal networks formed through branching and joining with other adjacent cell populations. T-cells added to the newly formed stromal networks migrated and attached to stromal cells, similar to the T-cell zones of the lymph nodes in vivo. Our results suggest that the constructed three-dimensional lymphoid stromal network can mimic the in vivo environment and allow the modeling of T-cell interaction in SLOs.

  14. A hybrid framework for improving recharge and discharge estimation for a three-dimensional groundwater flow model.

    PubMed

    Meyer, Scott C; Lin, Yu-Feng; Roadcap, George S

    2012-01-01

    We employed the ArcGIS plug-in package PRO-GRADE (Lin et al. 2009), developed for zonation of recharge/discharge (R/D) for modeling two-dimensional aquifer systems, to develop alternative R/D zonations for an existing three-dimensional groundwater flow model of a complex hydrogeologic setting. Our process began by intersecting PRO-GRADE output with the existing model's 4-zone R/D representation to develop a model having 12 R/D zones (R12) and then calibrating the resulting model using PEST. We then revised the R12 zonation using supplementary GIS data to develop a 51-zone R/D zonation (R51). From R51, we developed a series of daughter models having 40, 30, 28, and 18 R/D zones by removing zones from R51 if calibration resulted in little change in the zone's starting R/D rate and/or if the model was insensitive to the zone's R/D rate. For these models (R40N, R30N, R28N, and R18N), we used the ArcGIS Nibble tool to rapidly and consistently reassign model cells within eliminated zones of R51 to the zone of the nearest model cell in a retained zone having the same starting value. R12, R51, R40N, R30N, R28N, and R18N are all more accurate than the original model (R4), although improvements relative to stream discharge targets exceeded improvements relative to head targets. The models also executed with better numerical stability and less mass balance discrepancy than R4. These improvements demonstrate that R/D estimation in a complex shallow three-dimensional steady-state model can be improved with PRO-GRADE estimates of R/D when guided by calibration statistics and supplemental geographic data.

  15. A three-dimensional, time-dependent model of Mobile Bay

    NASA Technical Reports Server (NTRS)

    Pitts, F. H.; Farmer, R. C.

    1976-01-01

    A three-dimensional, time-variant mathematical model for momentum and mass transport in estuaries was developed and its solution implemented on a digital computer. The mathematical model is based on state and conservation equations applied to turbulent flow of a two-component, incompressible fluid having a free surface. Thus, bouyancy effects caused by density differences between the fresh and salt water, inertia from thare river and tidal currents, and differences in hydrostatic head are taken into account. The conservation equations, which are partial differential equations, are solved numerically by an explicit, one-step finite difference scheme and the solutions displayed numerically and graphically. To test the validity of the model, a specific estuary for which scaled model and experimental field data are available, Mobile Bay, was simulated. Comparisons of velocity, salinity and water level data show that the model is valid and a viable means of simulating the hydrodynamics and mass transport in non-idealized estuaries.

  16. THREE-DIMENSIONAL MODELING OF RELATIVISTIC COLLISIONLESS ION-ELECTRON SHOCKS

    SciTech Connect

    Haugboelle, Troels

    2011-10-01

    Two-dimensional (2D) modeling of collisionless shocks has been of tremendous importance in understanding the physics of nonlinear evolution, momentum transfer, and particle acceleration, but current computer capacities have now reached a point where three-dimensional (3D) modeling is becoming feasible. We present the first 3D model of a fully developed and relaxed relativistic ion-electron shock, and analyze and compare it to similar 2D models. Quantitative and qualitative differences are found with respect to the 2D models. The shock jump conditions are naturally different, because of the extra degree of freedom, but in addition it is found that strong parallel electric fields develop at the shock interface, the level of magnetic field energy is lower, and the non-thermal particle distribution is shallower with a power-law index of {approx}2.2.

  17. Coupling of three-dimensional field and human thermoregulatory models in a crowded enclosure

    SciTech Connect

    Xue, H.; Kang, Z.J.; Bong, T.Y.

    1999-11-12

    Health, comfort, and energy conservation are important factors to consider in the design of a building and its HVAC systems. Advanced tools are required to evaluate parameters regarding airflow, temperature, and humidity ratio in buildings, with the end results being better indoor air quality and thermal environment as well as increased confidence in the performance of buildings. A numerical model coupling the three-dimensional field and human thermoregulatory models is proposed and developed. A high-Re {kappa}-{epsilon} turbulence model is used for the field simulation. A modified 25-mode model of human thermoregulation is adopted to predict human thermal response in physiological parameters, such as body temperature and body heat loss. Distributions of air velocity, temperature, and moisture content are demonstrated in a crowded enclosure with mechanical ventilation under two ventilation rates. The results are analyzed and discussed. The coupling model is useful in assisting and verifying ventilation and air-conditioning system designs.

  18. Three-dimensional model and simulation of vacuum arcs under axial magnetic fields

    NASA Astrophysics Data System (ADS)

    Wang, Lijun; Jia, Shenli; Zhou, Xin; Wang, Haijing; Shi, Zongqian

    2012-01-01

    In this paper, a three-dimensional (3d) magneto-hydro-dynamic (MHD) model of axial magnetic field vacuum arcs (AMFVAs) is established. Based on this model, AMFVAs are simulated and analyzed. Three-dimensional spatial distributions of many important plasma parameters and electric characteristics in AMFVAs can be obtained, such as ion number density, ion temperature, electron temperature, plasma pressure, current densities along different directions (x, y, and z), ion velocities along different directions, electric fields strength along different directions, and so on. Simulation results show that there exist significant spiral-shaped rotational phenomena in the AMFVAs, this kind of rotational phenomenon also can be verified by the many related experiments (AMFVAs photographs, especially for stronger AMF strength). For current simulation results of AMFVAs, the maximal rotational velocity at anode side is about 1100 m/s. Radial electric field is increased from arc center to arc edge; axial electric field is decreased from cathode side to anode side. Radial electric field at arc edge can be larger than axial electric field. Azimuthal electric field in most regions is much smaller than radial and axial electric field, but it can reach about 1.19 kV/m. Radial magnetic field is the smallest one compared with other components, it reaches to maximum value at the position near to anode, it can influence arc characteristics.

  19. Three-dimensional transgenic cell model to quantify genotoxic effects of space environment

    NASA Astrophysics Data System (ADS)

    Gonda, S. R.; Wu, H.; Pingerelli, P. L.; Glickman, B. W.

    In this paper we describe a three-dimensional, multicellular tissue-equivalent model, produced in NASA-designed, rotating wall bioreactors using mammalian cells engineered for genomic containment of multiple copies of defined target genes for genotoxic assessment. Rat 2λ fibroblasts, genetically engineered to contain high-density target genes for mutagenesis (Stratagene, Inc., Austin, TX), were cocultured with human epithelial cells on Cytodex beads in the High Aspect Ratio Bioreactor (Synthecon, Inc, Houston, TX). Multi-bead aggregates were formed by day 5 following the complete covering of the beads by fibroblasts. Cellular retraction occurred 8-14 days after coculture initiation culminating in spheroids retaining few or no beads. Analysis of the resulting tissue assemblies revealed: multicellular spheroids, fibroblasts synthesized collagen, and cell viability was retained for the 30-day test period after removal from the bioreactor. Quantification of mutation at the LacI gene in Rat 2λ fibroblasts in spheroids exposed to 0-2 Gy neon using the Big Blue color assay (Stratagene, Inc.), revealed a linear dose-response for mutation induction. Limited sequencing analysis of mutant clones from 0.25 or 1 Gy exposures revealed a higher frequency of deletions and multiple base sequencing changes with increasing dose. These results suggest that the three-dimensional, multicellular tissue assembly model produced in NASA bioreactors are applicable to a wide variety of studies involving the quantification and identification of genotocity including measurement of the inherent damage incurred in Space.

  20. Calculation of vertical velocity in three-dimensional, shallow water equation, finite element models

    NASA Astrophysics Data System (ADS)

    Muccino, J. C.; Gray, W. G.; Foreman, M. G. G.

    1997-10-01

    Computation of vertical velocity within the confines of a three-dimensional, finite element model is a difficult but important task. This paper examines four approaches to the solution of the overdetermined system of equations arising when the first-order continuity equation is solved in conjunction with two boundary conditions. The traditional (TRAD) method neglects one boundary condition, solving the continuity equation with the remaining boundary condition. The vertical derivative of continuity (VDC) method involves solution of the second-order equation obtained by differentiation of the continuity equation with respect to the vertical co-ordinate. The least squares (LS) method minimizes the residuals of the continuity equation (in discrete form) and the two boundary conditions. The adjoint (ADJ) method minimizes the residuals of the continuity equation (in continuous form) and the two boundary conditions.Two domains are considered: a quarter-annular harbour and the southwest coast of Vancouver Island. Results indicate that the highest-quality solution is obtained with both LS and ADJ. Furthermore, ADJ requires less CPU and memory than LS. Therefore the optimal method for computation of vertical velocity in a three-dimensional finite element model is the adjoint (ADJ) method.

  1. Three-Dimensional Flow Separation Induced by a Model Vocal Fold Polyp

    NASA Astrophysics Data System (ADS)

    Stewart, Kelley C.; Erath, Byron D.; Plesniak, Michael W.

    2012-11-01

    The fluid-structure energy exchange process for normal speech has been studied extensively, but it is not well understood for pathological conditions. Polyps and nodules, which are geometric abnormalities that form on the medial surface of the vocal folds, can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. A recent in-vitro investigation of a model polyp in a driven vocal fold apparatus demonstrated that such a geometric abnormality considerably disrupts the glottal jet behavior and that this flow field adjustment was a likely reason for the severe degradation of the vocal quality in patients. Understanding of the formation and propagation of vortical structures from a geometric protuberance, and their subsequent impact on the aerodynamic loadings that drive vocal fold dynamic, is a critical component in advancing the treatment of this pathological condition. The present investigation concerns the three-dimensional flow separation induced by a wall-mounted prolate hemispheroid with a 2:1 aspect ratio in cross flow, i.e. a model vocal fold polyp. Unsteady three-dimensional flow separation and its impact of the wall pressure loading are examined using skin friction line visualization and wall pressure measurements. Supported by the National Science Foundation, Grant No. CBET-1236351 and GW Center for Biomimetics and Bioinspired Engineering (COBRE).

  2. Modeling self-excited combustion instabilities using a combination of two- and three-dimensional simulations

    NASA Astrophysics Data System (ADS)

    Harvazinski, Matthew Evan

    Self-excited combustion instabilities have been studied using a combination of two- and three-dimensional computational fluid dynamics (CFD) simulations. This work was undertaken to assess the ability of CFD simulations to generate the high-amplitude resonant combustion dynamics without external forcing or a combustion response function. Specifically, detached eddy simulations (DES), which allow for significantly coarser grid resolutions in wall bounded flows than traditional large eddy simulations (LES), were investigated for their capability of simulating the instability. A single-element laboratory rocket combustor which produces self-excited longitudinal instabilities is used for the configuration. The model rocket combustor uses an injector configuration based on practical oxidizer-rich staged-combustion devices; a sudden expansion combustion section; and uses decomposed hydrogen peroxide as the oxidizer and gaseous methane as the fuel. A better understanding of the physics has been achieved using a series of diagnostics. Standard CFD outputs like instantaneous and time averaged flowfield outputs are combined with other tools, like the Rayleigh index to provide additional insight. The Rayleigh index is used to identify local regions in the combustor which are responsible for driving and damping the instability. By comparing the Rayleigh index to flowfield parameters it is possible to connect damping and driving to specific flowfield conditions. A cost effective procedure to compute multidimensional local Rayleigh index was developed. This work shows that combustion instabilities can be qualitatively simulated using two-dimensional axisymmetric simulations for fuel rich operating conditions. A full three-dimensional simulation produces a higher level of instability which agrees quite well with the experimental results. In addition to matching the level of instability the three-dimensional simulation also predicts the harmonic nature of the instability that is

  3. Three-Dimensional Finite Element Modeling of Electromagnetic Nondestructive Testing Phenomena.

    NASA Astrophysics Data System (ADS)

    Ida, Nathan

    Electromagnetic methods of nondestructive testing are widely used in various industries for characterization of material properties and detection of flaws. These methods are based on measurable changes in the electrical and magnetic properties of materials caused by the interaction with applied and induced fields. Analytical approaches to the modeling of electromagnetic field/defect interaction have largely been unsuccessful due to the awkward boundaries of realistic three dimensional defects and the need for simplifying assumptions. General theoretical models are needed, capable of handling complicated test geometries in order to understand the physics of field interactions with defects, to simulate testing situations which are difficult and/or expensive to replicate and to provide training data for automated defect characterization schemes. Numerical models based on a finite element formulation of the classical Maxwell's equations have the ability to overcome these difficulties. This thesis describes the three dimensional finite element formulation of the magnetostatic and eddy current equations and its use in theoretically modeling leakage fields and impedances of eddy current probes in the presence of three dimensional defects. The formulation is based on an energy balance concept, resulting in a system of linear equations. These equations are solved for the magnetic vector potential from which other quantities such as flux densities and probe impedances are calculated. The model presented can accomodate spatial nonlinearities but not field dependence of permeability. The validity of the numerical model is established by comparison with two dimensional, finite element solutions and to experimental data. The method is applied to predict leakage field profiles from defects in steel bars and eddy current probe impedances in geometries relating to nuclear power plant steam generators. The errors encountered in these calculations are mainly due to limitations on

  4. Three-dimensional models of conventional and vertical junction laser-photovoltaic energy converters

    NASA Technical Reports Server (NTRS)

    Heinbockel, John H.; Walker, Gilbert H.

    1988-01-01

    Three-dimensional models of both conventional planar junction and vertical junction photovoltaic energy converters have been constructed. The models are a set of linear partial differential equations and take into account many photoconverter design parameters. The model is applied to Si photoconverters; however, the model may be used with other semiconductors. When used with a Nd laser, the conversion efficiency of the Si vertical junction photoconverter is 47 percent, whereas the efficiency for the conventional planar Si photoconverter is only 17 percent. A parametric study of the Si vertical junction photoconverter is then done in order to describe the optimum converter for use with the 1.06-micron Nd laser. The efficiency of this optimized vertical junction converter is 44 percent at 1 kW/sq cm.

  5. Coupling of discrete random walks and continuous modeling for three-dimensional tumor-induced angiogenesis

    NASA Astrophysics Data System (ADS)

    Vilanova, Guillermo; Colominas, Ignasi; Gomez, Hector

    2014-03-01

    The growth of new vascular networks from pre-existing capillaries (angiogenesis) plays a pivotal role in tumor development. Mathematical modeling of tumor-induced angiogenesis may help understand the underlying biology of the process and provide new hypotheses for experimentation. Here, we couple an existing deterministic continuum theory with a discrete random walk, proposing a new model that accounts for chemotactic and haptotactic cellular migration. We propose an efficient numerical method to approximate the solution of the model. The accuracy, stability and effectiveness of our algorithms permitted us to perform large-scale three-dimensional simulations which, in contrast to two-dimensional calculations, show a topological complexity similar to that found in experiments. Finally, we use our model and simulations to investigate the role of haptotaxis and chemotaxis in the mobility of tip endothelial cells and its influence in the final vascular patterns.

  6. Hydrophobicity within the three-dimensional Mercedes-Benz model: Potential of mean force

    NASA Astrophysics Data System (ADS)

    Dias, Cristiano L.; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S.; Karttunen, Mikko

    2011-02-01

    We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

  7. Analytical model for three-dimensional Mercedes-Benz water molecules

    PubMed Central

    Urbic, T.

    2013-01-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature. PMID:23005100

  8. Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force.

    PubMed

    Dias, Cristiano L; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S; Karttunen, Mikko

    2011-02-14

    We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model.

  9. Analytical model for three-dimensional Mercedes-Benz water molecules

    NASA Astrophysics Data System (ADS)

    Urbic, T.

    2012-06-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.

  10. Analytical model for three-dimensional Mercedes-Benz water molecules.

    PubMed

    Urbic, T

    2012-06-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.

  11. Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

    DOE PAGES

    Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; Gibbs, Paul J.; Gibbs, John W.; Karma, Alain

    2015-05-27

    We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. The focus is on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues formore » investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.« less

  12. Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

    SciTech Connect

    Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; Gibbs, Paul J.; Gibbs, John W.; Karma, Alain

    2015-05-27

    We present a three-dimensional extension of the multiscale dendritic needle network (DNN) model. This approach enables quantitative simulations of the unsteady dynamics of complex hierarchical networks in spatially extended dendritic arrays. We apply the model to directional solidification of Al-9.8 wt.%Si alloy and directly compare the model predictions with measurements from experiments with in situ x-ray imaging. The focus is on the dynamical selection of primary spacings over a range of growth velocities, and the influence of sample geometry on the selection of spacings. Simulation results show good agreement with experiments. The computationally efficient DNN model opens new avenues for investigating the dynamics of large dendritic arrays at scales relevant to solidification experiments and processes.

  13. Three-dimensional ray-tracing model for the study of advanced refractive errors in keratoconus.

    PubMed

    Schedin, Staffan; Hallberg, Per; Behndig, Anders

    2016-01-20

    We propose a numerical three-dimensional (3D) ray-tracing model for the analysis of advanced corneal refractive errors. The 3D modeling was based on measured corneal elevation data by means of Scheimpflug photography. A mathematical description of the measured corneal surfaces from a keratoconus (KC) patient was used for the 3D ray tracing, based on Snell's law of refraction. A model of a commercial intraocular lens (IOL) was included in the analysis. By modifying the posterior IOL surface, it was shown that the imaging quality could be significantly improved. The RMS values were reduced by approximately 50% close to the retina, both for on- and off-axis geometries. The 3D ray-tracing model can constitute a basis for simulation of customized IOLs that are able to correct the advanced, irregular refractive errors in KC.

  14. A Three-Dimensional Mediastinal Model Created with Rapid Prototyping in a Patient with Ectopic Thymoma

    PubMed Central

    Nakada, Takeo; Inagaki, Takuya

    2014-01-01

    Preoperative three-dimensional (3D) imaging of a mediastinal tumor using two-dimensional (2D) axial computed tomography is sometimes difficult, and an unexpected appearance of the tumor may be encountered during surgery. In order to evaluate the preoperative feasibility of a 3D mediastinal model that used the rapid prototyping technique, we created a model and report its results. The 2D image showed some of the relationship between the tumor and the pericardium, but the 3D mediastinal model that was created using the rapid prototyping technique showed the 3D lesion in the outer side of the extrapericardium. The patient underwent a thoracoscopic resection of the tumor, and the pathological examination showed a rare middle mediastinal ectopic thymoma. We believe that the construction of mediastinal models is useful for thoracoscopic surgery and other complicated surgeries of the chest diseases. PMID:24633133

  15. Development of a three dimensional numerical water quality model for continental shelf applications

    NASA Technical Reports Server (NTRS)

    Spaulding, M.; Hunter, D.

    1975-01-01

    A model to predict the distribution of water quality parameters in three dimensions was developed. The mass transport equation was solved using a non-dimensional vertical axis and an alternating-direction-implicit finite difference technique. The reaction kinetics of the constituents were incorporated into a matrix method which permits computation of the interactions of multiple constituents. Methods for the computation of dispersion coefficients and coliform bacteria decay rates were determined. Numerical investigations of dispersive and dissipative effects showed that the three-dimensional model performs as predicted by analysis of simpler cases. The model was then applied to a two dimensional vertically averaged tidal dynamics model for the Providence River. It was also extended to a steady state application by replacing the time step with an iteration sequence. This modification was verified by comparison to analytical solutions and applied to a river confluence situation.

  16. Three-dimensional Monte Carlo model of pulsed-laser treatment of cutaneous vascular lesions

    NASA Astrophysics Data System (ADS)

    Milanič, Matija; Majaron, Boris

    2011-12-01

    We present a three-dimensional Monte Carlo model of optical transport in skin with a novel approach to treatment of side boundaries of the volume of interest. This represents an effective way to overcome the inherent limitations of ``escape'' and ``mirror'' boundary conditions and enables high-resolution modeling of skin inclusions with complex geometries and arbitrary irradiation patterns. The optical model correctly reproduces measured values of diffuse reflectance for normal skin. When coupled with a sophisticated model of thermal transport and tissue coagulation kinetics, it also reproduces realistic values of radiant exposure thresholds for epidermal injury and for photocoagulation of port wine stain blood vessels in various skin phototypes, with or without application of cryogen spray cooling.

  17. Analytical model for three-dimensional Mercedes-Benz water molecules.

    PubMed

    Urbic, T

    2012-06-01

    We developed a statistical model which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen-bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen-bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes-Benz model of water. We explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility as a function of temperature and pressure. We found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature. PMID:23005100

  18. Hydrophobicity within the three-dimensional Mercedes-Benz model: potential of mean force.

    PubMed

    Dias, Cristiano L; Hynninen, Teemu; Ala-Nissila, Tapio; Foster, Adam S; Karttunen, Mikko

    2011-02-14

    We use the three-dimensional Mercedes-Benz model for water and Monte Carlo simulations to study the structure and thermodynamics of the hydrophobic interaction. Radial distribution functions are used to classify different cases of the interaction, namely, contact configurations, solvent separated configurations, and desolvation configurations. The temperature dependence of these cases is shown to be in qualitative agreement with atomistic models of water. In particular, while the energy for the formation of contact configurations is favored by entropy, its strengthening with increasing temperature is accounted for by enthalpy. This is consistent with our simulated heat capacity. An important feature of the model is that it can be used to account for well-converged thermodynamics quantities, e.g., the heat capacity of transfer. Microscopic mechanisms for the temperature dependence of the hydrophobic interaction are discussed at the molecular level based on the conceptual simplicity of the model. PMID:21322739

  19. A three-dimensional meso-scale computer modeling for bubble growth in metals

    NASA Astrophysics Data System (ADS)

    Suzudo, T.; Kaburaki, H.; Itakura, M.; Wakai, E.

    2008-07-01

    A new meso-scale three-dimensional computer model has been proposed to enhance the modeling capability of the bubble growth in metals, particularly helium bubble growth under conditions of post-irradiation annealing. We assume that the bubble growth is modeled by a process driven by energy minimization of the surface energy and thermal fluctuation within the framework of a Monte Carlo simulation method. We found that it is possible to simulate growing bubbles following the ideal gas law and in equilibrium with the surface tension. The simulation results show good agreement with some experimental evidence, in particular, of the log-normal bubble-size distribution. The extension of the model to the bubble growth on grain boundaries with reference to helium embrittlement has succeeded in reproducing a particular bubble shape observed in experiments.

  20. Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model

    USGS Publications Warehouse

    Warner, J.C.; Sherwood, C.R.; Signell, R.P.; Harris, C.K.; Arango, H.G.

    2008-01-01

    We are developing a three-dimensional numerical model that implements algorithms for sediment transport and evolution of bottom morphology in the coastal-circulation model Regional Ocean Modeling System (ROMS v3.0), and provides a two-way link between ROMS and the wave model Simulating Waves in the Nearshore (SWAN) via the Model-Coupling Toolkit. The coupled model is applicable for fluvial, estuarine, shelf, and nearshore (surfzone) environments. Three-dimensional radiation-stress terms have been included in the momentum equations, along with effects of a surface wave roller model. The sediment-transport algorithms are implemented for an unlimited number of user-defined non-cohesive sediment classes. Each class has attributes of grain diameter, density, settling velocity, critical stress threshold for erosion, and erodibility constant. Suspended-sediment transport in the water column is computed with the same advection-diffusion algorithm used for all passive tracers and an additional algorithm for vertical settling that is not limited by the CFL criterion. Erosion and deposition are based on flux formulations. A multi-level bed framework tracks the distribution of every size class in each layer and stores bulk properties including layer thickness, porosity, and mass, allowing computation of bed morphology and stratigraphy. Also tracked are bed-surface properties including active-layer thickness, ripple geometry, and bed roughness. Bedload transport is calculated for mobile sediment classes in the top layer. Bottom-boundary layer submodels parameterize wave-current interactions that enhance bottom stresses and thereby facilitate sediment transport and increase bottom drag, creating a feedback to the circulation. The model is demonstrated in a series of simple test cases and a realistic application in Massachusetts Bay. ?? 2008 Elsevier Ltd. All rights reserved.

  1. Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model

    NASA Astrophysics Data System (ADS)

    Warner, John C.; Sherwood, Christopher R.; Signell, Richard P.; Harris, Courtney K.; Arango, Hernan G.

    2008-10-01

    We are developing a three-dimensional numerical model that implements algorithms for sediment transport and evolution of bottom morphology in the coastal-circulation model Regional Ocean Modeling System (ROMS v3.0), and provides a two-way link between ROMS and the wave model Simulating Waves in the Nearshore (SWAN) via the Model-Coupling Toolkit. The coupled model is applicable for fluvial, estuarine, shelf, and nearshore (surfzone) environments. Three-dimensional radiation-stress terms have been included in the momentum equations, along with effects of a surface wave roller model. The sediment-transport algorithms are implemented for an unlimited number of user-defined non-cohesive sediment classes. Each class has attributes of grain diameter, density, settling velocity, critical stress threshold for erosion, and erodibility constant. Suspended-sediment transport in the water column is computed with the same advection-diffusion algorithm used for all passive tracers and an additional algorithm for vertical settling that is not limited by the CFL criterion. Erosion and deposition are based on flux formulations. A multi-level bed framework tracks the distribution of every size class in each layer and stores bulk properties including layer thickness, porosity, and mass, allowing computation of bed morphology and stratigraphy. Also tracked are bed-surface properties including active-layer thickness, ripple geometry, and bed roughness. Bedload transport is calculated for mobile sediment classes in the top layer. Bottom-boundary layer submodels parameterize wave-current interactions that enhance bottom stresses and thereby facilitate sediment transport and increase bottom drag, creating a feedback to the circulation. The model is demonstrated in a series of simple test cases and a realistic application in Massachusetts Bay.

  2. Three-dimensional delayed-detonation models with nucleosynthesis for Type Ia supernovae

    NASA Astrophysics Data System (ADS)

    Seitenzahl, Ivo R.; Ciaraldi-Schoolmann, Franco; Röpke, Friedrich K.; Fink, Michael; Hillebrandt, Wolfgang; Kromer, Markus; Pakmor, Rüdiger; Ruiter, Ashley J.; Sim, Stuart A.; Taubenberger, Stefan

    2013-02-01

    We present results for a suite of 14 three-dimensional, high-resolution hydrodynamical simulations of delayed-detonation models of Type Ia supernova (SN Ia) explosions. This model suite comprises the first set of three-dimensional SN Ia simulations with detailed isotopic yield information. As such, it may serve as a data base for Chandrasekhar-mass delayed-detonation model nucleosynthetic yields and for deriving synthetic observables such as spectra and light curves. We employ a physically motivated, stochastic model based on turbulent velocity fluctuations and fuel density to calculate in situ the deflagration-to-detonation transition probabilities. To obtain different strengths of the deflagration phase and thereby different degrees of pre-expansion, we have chosen a sequence of initial models with 1, 3, 5, 10, 20, 40, 100, 150, 200, 300 and 1600 (two different realizations) ignition kernels in a hydrostatic white dwarf with a central density of 2.9 × 109 g cm-3, as well as one high central density (5.5 × 109 g cm-3) and one low central density (1.0 × 109 g cm-3) rendition of the 100 ignition kernel configuration. For each simulation, we determined detailed nucleosynthetic yields by post-processing 106 tracer particles with a 384 nuclide reaction network. All delayed-detonation models result in explosions unbinding the white dwarf, producing a range of 56Ni masses from 0.32 to 1.11 M⊙. As a general trend, the models predict that the stable neutron-rich iron-group isotopes are not found at the lowest velocities, but rather at intermediate velocities (˜3000-10 000 km s-1) in a shell surrounding a 56Ni-rich core. The models further predict relatively low-velocity oxygen and carbon, with typical minimum velocities around 4000 and 10 000 km s-1, respectively.

  3. Intraglottal pressures in a three-dimensional model with a non-rectangular glottal shape

    PubMed Central

    Scherer, Ronald C.; Torkaman, Saeed; Kucinschi, Bogdan R.; Afjeh, Abdollah A.

    2010-01-01

    This study used a symmetric, three-dimensional, physical model of the larynx called M6 in which the transverse plane of the glottis is formed by sinusoidal arcs for each medial vocal fold surface, creating a maximum glottal width of 0.16 cm at the location of the minimal glottal area. Three glottal angles were studied: convergent 10°, uniform (0°), and divergent 10°. Fourteen pressure taps were incorporated in the upstream-downstream direction on the vocal fold surface at three coronal locations, at the one-fourth, one-half, and three-fourths distances in the anterior-posterior direction of the glottis. The computational software FLUENT was used to compare and augment the data for these cases. Near the glottal entrance, the pressures were similar across the three locations for the uniform case; however, for the convergent case the middle pressure distribution was lower by 4% of the transglottal pressure, and lower by about 2% for the divergent case. Also, there were significant secondary velocities toward the center from both the anterior commissure and vocal process regions (of as much as approximately 10% of the axial velocities). Thus, the three dimensionality created relatively small pressure gradients and significant secondary velocities anteriorly-posteriorly within the glottis. PMID:20707452

  4. Mechanism of drag reduction on a three-dimensional model vehicle using a passive control device

    NASA Astrophysics Data System (ADS)

    Yi, Wook; Sagong, Woong; Choi, Haecheon

    2007-11-01

    It has been well known that the boat-tail device reduces drag on a three-dimensional vehicle. However, its detailed mechanism is not clearly known yet. To understand this mechanism, we conduct an experiment for flow over a three-dimensional model vehicle in ground proximity. We consider various lengths (l/H = 0.1 ˜0.5) and slant angles (θ=0^o ˜40^o) of the boat tail, and conduct velocity measurements near the boat tail and oil visualizations on the boat-tail surface. We find that the slant angle is an important parameter for drag reduction. The maximum drag reduction occurs at θ=12.5^o, 15^o and 15^o for l/H = 0.1, 0.3 and 0.5, respectively, and the amounts of maximum drag reduction are 20, 41 and 45%. For the case of l/H = 0.3, separation starts to occur from θ= 6^o at the leading edge of the boat tail. This separated flow reattaches on the boat-tail surface and forms a small secondary separation bubble, which provides strong near-wall momentum and delays main separation down to the trailing edge of boat tail. The size of secondary separation bubble increases with increasing θ. At θ>16^o, main separation occurs at the leading edge of boat tail, and drag increases from the minimum value and reaches that of no control at large θ's.

  5. Generation of three-dimensional multiple spheroid model of olfactory ensheathing cells using floating liquid marbles

    PubMed Central

    Vadivelu, Raja K.; Ooi, Chin H.; Yao, Rebecca-Qing; Tello Velasquez, Johana; Pastrana, Erika; Diaz-Nido, Javier; Lim, Filip; Ekberg, Jenny A. K.; Nguyen, Nam-Trung; St John, James A.

    2015-01-01

    We describe a novel protocol for three-dimensional culturing of olfactory ensheathing cells (OECs), which can be used to understand how OECs interact with other cells in three dimensions. Transplantation of OECs is being trialled for repair of the paralysed spinal cord, with promising but variable results and thus the therapy needs improving. To date, studies of OEC behaviour in a multicellular environment have been hampered by the lack of suitable three-dimensional cell culture models. Here, we exploit the floating liquid marble, a liquid droplet coated with hydrophobic powder and placed on a liquid bath. The presence of the liquid bath increases the humidity and minimises the effect of evaporation. Floating liquid marbles allow the OECs to freely associate and interact to produce OEC spheroids with uniform shapes and sizes. In contrast, a sessile liquid marble on a solid surface suffers from evaporation and the cells aggregate with irregular shapes. We used floating liquid marbles to co-culture OECs with Schwann cells and astrocytes which formed natural structures without the confines of gels or bounding layers. This protocol can be used to determine how OECs and other cell types associate and interact while forming complex cell structures. PMID:26462469

  6. Vestibular coriolis effect differences modeled with three-dimensional linear-angular interactions.

    PubMed

    Holly, Jan E

    2004-01-01

    The vestibular coriolis (or "cross-coupling") effect is traditionally explained by cross-coupled angular vectors, which, however, do not explain the differences in perceptual disturbance under different acceleration conditions. For example, during head roll tilt in a rotating chair, the magnitude of perceptual disturbance is affected by a number of factors, including acceleration or deceleration of the chair rotation or a zero-g environment. Therefore, it has been suggested that linear-angular interactions play a role. The present research investigated whether these perceptual differences and others involving linear coriolis accelerations could be explained under one common framework: the laws of motion in three dimensions, which include all linear-angular interactions among all six components of motion (three angular and three linear). The results show that the three-dimensional laws of motion predict the differences in perceptual disturbance. No special properties of the vestibular system or nervous system are required. In addition, simulations were performed with angular, linear, and tilt time constants inserted into the model, giving the same predictions. Three-dimensional graphics were used to highlight the manner in which linear-angular interaction causes perceptual disturbance, and a crucial component is the Stretch Factor, which measures the "unexpected" linear component.

  7. Vestibular coriolis effect differences modeled with three-dimensional linear-angular interactions.

    PubMed

    Holly, Jan E

    2004-01-01

    The vestibular coriolis (or "cross-coupling") effect is traditionally explained by cross-coupled angular vectors, which, however, do not explain the differences in perceptual disturbance under different acceleration conditions. For example, during head roll tilt in a rotating chair, the magnitude of perceptual disturbance is affected by a number of factors, including acceleration or deceleration of the chair rotation or a zero-g environment. Therefore, it has been suggested that linear-angular interactions play a role. The present research investigated whether these perceptual differences and others involving linear coriolis accelerations could be explained under one common framework: the laws of motion in three dimensions, which include all linear-angular interactions among all six components of motion (three angular and three linear). The results show that the three-dimensional laws of motion predict the differences in perceptual disturbance. No special properties of the vestibular system or nervous system are required. In addition, simulations were performed with angular, linear, and tilt time constants inserted into the model, giving the same predictions. Three-dimensional graphics were used to highlight the manner in which linear-angular interaction causes perceptual disturbance, and a crucial component is the Stretch Factor, which measures the "unexpected" linear component. PMID:15735327

  8. Generation of three-dimensional multiple spheroid model of olfactory ensheathing cells using floating liquid marbles

    NASA Astrophysics Data System (ADS)

    Vadivelu, Raja K.; Ooi, Chin H.; Yao, Rebecca-Qing; Tello Velasquez, Johana; Pastrana, Erika; Diaz-Nido, Javier; Lim, Filip; Ekberg, Jenny A. K.; Nguyen, Nam-Trung; St John, James A.

    2015-10-01

    We describe a novel protocol for three-dimensional culturing of olfactory ensheathing cells (OECs), which can be used to understand how OECs interact with other cells in three dimensions. Transplantation of OECs is being trialled for repair of the paralysed spinal cord, with promising but variable results and thus the therapy needs improving. To date, studies of OEC behaviour in a multicellular environment have been hampered by the lack of suitable three-dimensional cell culture models. Here, we exploit the floating liquid marble, a liquid droplet coated with hydrophobic powder and placed on a liquid bath. The presence of the liquid bath increases the humidity and minimises the effect of evaporation. Floating liquid marbles allow the OECs to freely associate and interact to produce OEC spheroids with uniform shapes and sizes. In contrast, a sessile liquid marble on a solid surface suffers from evaporation and the cells aggregate with irregular shapes. We used floating liquid marbles to co-culture OECs with Schwann cells and astrocytes which formed natural structures without the confines of gels or bounding layers. This protocol can be used to determine how OECs and other cell types associate and interact while forming complex cell structures.

  9. Three-fluid, three-dimensional magnetohydrodynamic solar wind model with eddy viscosity and turbulent resistivity

    SciTech Connect

    Usmanov, Arcadi V.; Matthaeus, William H.; Goldstein, Melvyn L.

    2014-06-10

    We have developed a three-fluid, three-dimensional magnetohydrodynamic solar wind model that incorporates turbulence transport, eddy viscosity, turbulent resistivity, and turbulent heating. The solar wind plasma is described as a system of co-moving solar wind protons, electrons, and interstellar pickup protons, with separate energy equations for each species. Numerical steady-state solutions of Reynolds-averaged solar wind equations coupled with turbulence transport equations for turbulence energy, cross helicity, and correlation length are obtained by the time relaxation method in the corotating with the Sun frame of reference in the region from 0.3 to 100 AU (but still inside the termination shock). The model equations include the effects of electron heat conduction, Coulomb collisions, photoionization of interstellar hydrogen atoms and their charge exchange with the solar wind protons, turbulence energy generation by pickup protons, and turbulent heating of solar wind protons and electrons. The turbulence transport model is based on the Reynolds decomposition and turbulence phenomenologies that describe the conversion of fluctuation energy into heat due to a turbulent cascade. In addition to using separate energy equations for the solar wind protons and electrons, a significant improvement over our previous work is that the turbulence model now uses an eddy viscosity approximation for the Reynolds stress tensor and the mean turbulent electric field. The approximation allows the turbulence model to account for driving of turbulence by large-scale velocity gradients. Using either a dipole approximation for the solar magnetic field or synoptic solar magnetograms from the Wilcox Solar Observatory for assigning boundary conditions at the coronal base, we apply the model to study the global structure of the solar wind and its three-dimensional properties, including embedded turbulence, heating, and acceleration throughout the heliosphere. The model results are

  10. Spherical wave reflection in layered media with rough interfaces: Three-dimensional modeling.

    PubMed

    Pinson, Samuel; Cordioli, Julio; Guillon, Laurent

    2016-08-01

    In the context of sediment characterization, layer interface roughnesses may be responsible for sound-speed profile measurement uncertainties. To study the roughness influence, a three-dimensional (3D) modeling of a layered seafloor with rough interfaces is necessary. Although roughness scattering has an abundant literature, 3D modeling of spherical wave reflection on rough interfaces is generally limited to a single interface (using Kirchhoff-Helmholtz integral) or computationally expensive techniques (finite difference or finite element method). In this work, it is demonstrated that the wave reflection over a layered medium with irregular interfaces can be modeled as a sum of integrals over each interface. The main approximations of the method are the tangent-plane approximation, the Born approximation (multiple reflection between interfaces are neglected) and flat-interface approximation for the transmitted waves into the sediment. The integration over layer interfaces results in a method with reasonable computation cost.

  11. Intracellular Ca 2+ nonlinear wave behaviours in a three dimensional ventricular cell model

    NASA Astrophysics Data System (ADS)

    Li, Pan; Holden, Arun V.

    2009-06-01

    Intracellular Ca 2+ activity regulates a wide range of cellular biochemical processes; in muscle cells, it links membrane excitation to contraction. Ca 2+ dynamics includes both synchronous oscillations, and nonlinear wave phenomena, both arising from the superposition of spatially localised stochastic events, such as Ca 2+ sparks. We incorporated individualised cell geometry reconstructed from confocal microscopy with realistic spatial distribution of RyR clusters into the three dimensional ventricular cell model, and reproduced complex spatio-temporal intracellular wave patterns from Ca 2+ sparks. We also introduced a detailed nuclear Ca 2+ handing model to simulate prolonged nuclear Ca 2+ transient, and study the effects of cytosolic-nuclear coupling on intracellular Ca 2+ dynamics. The model provides a computational platform to study intracellular Ca 2+ with the ability to interact with experimental measurements of subcellular structures, and can be modified for other cell types.

  12. Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets

    PubMed Central

    Crivoi, A.; Duan, Fei

    2014-01-01

    The residual deposits usually left near the contact line after pinned sessile colloidal droplet evaporation are commonly known as a “coffee-ring” effect. However, there were scarce attempts to simulate the effect, and the realistic fully three-dimensional (3D) model is lacking since the complex drying process seems to limit the further investigation. Here we develop a stochastic method to model the particle deposition in evaporating a pinned sessile colloidal droplet. The 3D Monte Carlo model is developed in the spherical-cap-shaped droplet. In the algorithm, the analytical equations of fluid flow are used to calculate the probability distributions for the biased random walk, associated with the drift-diffusion equations. We obtain the 3D coffee-ring structures as the final results of the simulation and analyze the dependence of the ring profile on the particle volumetric concentration and sticking probability. PMID:24603647

  13. Three-dimensional numerical modelling of gas discharges at atmospheric pressure incorporating photoionization phenomena

    NASA Astrophysics Data System (ADS)

    Papageorgiou, L.; Metaxas, A. C.; Georghiou, G. E.

    2011-02-01

    A three-dimensional (3D) numerical model for the characterization of gas discharges in air at atmospheric pressure incorporating photoionization through the solution of the Helmholtz equation is presented. Initially, comparisons with a two-dimensional (2D) axi-symmetric model are performed in order to assess the validity of the model. Subsequently several discharge instabilities (plasma spots and low pressure inhomogeneities) are considered in order to study their effect on streamer branching and off-axis propagation. Depending on the magnitude and position of the plasma spot, deformations and off-axis propagation of the main discharge channel were obtained. No tendency for branching in small (of the order of 0.1 cm) overvolted discharge gaps was observed.

  14. Conversion of the Big Hill geological site characterization report to a three-dimensional model.

    SciTech Connect

    Stein, Joshua S.; Rautman, Christopher Arthur

    2003-02-01

    The Big Hill salt dome, located in southeastern Texas, is home to one of four underground oil-storage facilities managed by the U. S. Department of Energy Strategic Petroleum Reserve (SPR) Program. Sandia National Laboratories, as the geotechnical advisor to the SPR, conducts site-characterization investigations and other longer-term geotechnical and engineering studies in support of the program. This report describes the conversion of two-dimensional geologic interpretations of the Big Hill site into three-dimensional geologic models. The new models include the geometry of the salt dome, the surrounding sedimentary units, mapped faults, and the 14 oil storage caverns at the site. This work provides a realistic and internally consistent geologic model of the Big Hill site that can be used in support of future work.

  15. Conversion of the Bryan Mound geological site characterization reports to a three-dimensional model.

    SciTech Connect

    Stein, Joshua S.; Rautman, Christopher Arthur

    2005-04-01

    The Bryan Mound salt dome, located near Freeport, Texas, is home to one of four underground crude oil-storage facilities managed by the U. S. Department of Energy Strategic Petroleum Reserve (SPR) Program. Sandia National Laboratories, as the geotechnical advisor to the SPR, conducts site-characterization investigations and other longer-term geotechnical and engineering studies in support of the program. This report describes the conversion of two-dimensional geologic interpretations of the Bryan Mound site into three-dimensional geologic models. The new models include the geometry of the salt dome, the surrounding sedimentary units, mapped faults, and the 20 oil-storage caverns at the site. This work provides an internally consistent geologic model of the Bryan Mound site that can be used in support of future work.

  16. Spherical wave reflection in layered media with rough interfaces: Three-dimensional modeling.

    PubMed

    Pinson, Samuel; Cordioli, Julio; Guillon, Laurent

    2016-08-01

    In the context of sediment characterization, layer interface roughnesses may be responsible for sound-speed profile measurement uncertainties. To study the roughness influence, a three-dimensional (3D) modeling of a layered seafloor with rough interfaces is necessary. Although roughness scattering has an abundant literature, 3D modeling of spherical wave reflection on rough interfaces is generally limited to a single interface (using Kirchhoff-Helmholtz integral) or computationally expensive techniques (finite difference or finite element method). In this work, it is demonstrated that the wave reflection over a layered medium with irregular interfaces can be modeled as a sum of integrals over each interface. The main approximations of the method are the tangent-plane approximation, the Born approximation (multiple reflection between interfaces are neglected) and flat-interface approximation for the transmitted waves into the sediment. The integration over layer interfaces results in a method with reasonable computation cost. PMID:27586741

  17. An unstructured grid, three-dimensional model based on the shallow water equations

    USGS Publications Warehouse

    Casulli, V.; Walters, R.A.

    2000-01-01

    A semi-implicit finite difference model based on the three-dimensional shallow water equations is modified to use unstructured grids. There are obvious advantages in using unstructured grids in problems with a complicated geometry. In this development, the concept of unstructured orthogonal grids is introduced and applied to this model. The governing differential equations are discretized by means of a semi-implicit algorithm that is robust, stable and very efficient. The resulting model is relatively simple, conserves mass, can fit complicated boundaries and yet is sufficiently flexible to permit local mesh refinements in areas of interest. Moreover, the simulation of the flooding and drying is included in a natural and straightforward manner. These features are illustrated by a test case for studies of convergence rates and by examples of flooding on a river plain and flow in a shallow estuary. Copyright ?? 2000 John Wiley & Sons, Ltd.

  18. Quasi-Three-Dimensional Mathematical Modeling of Morphological Processes Based on Equilibrium Sediment Transport

    NASA Astrophysics Data System (ADS)

    Charafi, My. M.; Sadok, A.; Kamal, A.; Menai, A.

    A quasi-three-dimensional mathematical model has been developed to study the morphological processes based on equilibrium sediment transport method. The flow velocities are computed by a two-dimensional horizontal depth-averaged flow model (H2D) in combination with logarithmic velocity profiles. The transport of sediment particles by a flow water has been considered in the form of bed load and suspended load. The bed load transport rate is defined as the transport of particles by rolling and saltating along the bed surface and is given by the Van Rijn relationship (1987). The equilibrium suspended load transport is described in terms of an equilibrium sediment concentration profile (ce) and a logarithmic velocity (u). Based on the equilibrium transport, the bed change rate is given by integration of the sediment mass-balance equation. The model results have been compared with a Van Rijn results (equilibrium approach) and good agreement has been found.

  19. A new three-dimensional electromechanical impedance model for an embedded dual-PZT transducer

    NASA Astrophysics Data System (ADS)

    Wang, Dansheng; Li, Zhi; Zhu, Hongping

    2016-07-01

    In the past twenty years, the electromechanical (EM) impedance technique has been investigated extensively in the mechanical, aviation and civil engineering fields. Many different EM impedance models have been proposed to characterize the interaction between the surface-bonded PZT transducer and the host structure. This paper formulates a new three-dimensional EM impedance model characterizing the interaction between an embedded circle dual-PZT transducer and the host structure based on the effective impedance concept. The proposed model is validated by experimental results from a group of smart cement cubes, in which three circle dual-PZT transducers are embedded respectively. In addition, a new EM impedance measuring method for the dual-PZT transducer is also introduced. In the measuring method, only a common signal generator and an oscilloscope are needed, by which the exciting and receiving voltage signals are obtained respectively. Combined with fast Fourier transform the EM impedance signatures of the dual-PZT transducers are obtained.

  20. A three-dimensional, finite element model for coastal and estuarine circulation

    USGS Publications Warehouse

    Walters, R.A.

    1992-01-01

    This paper describes the development and application of a three-dimensional model for coastal and estuarine circulation. The model uses a harmonic expansion in time and a finite element discretization in space. All nonlinear terms are retained, including quadratic bottom stress, advection and wave transport (continuity nonlinearity). The equations are solved as a global and a local problem, where the global problem is the solution of the wave equation formulation of the shallow water equations, and the local problem is the solution of the momentum equation for the vertical velocity profile. These equations are coupled to the advection-diffusion equation for salt so that density gradient forcing is included in the momentum equations. The model is applied to a study of Delaware Bay, U.S.A., where salinity intrusion is the primary focus. ?? 1991.

  1. Conversion of the West Hackberry geological site characterization report to a three-dimensional model.

    SciTech Connect

    Stein, Joshua S.; Rautman, Christopher Arthur; Snider, Anna C.

    2004-08-01

    The West Hackberry salt dome, in southwestern Louisiana, is one of four underground oil-storage facilities managed by the U. S. Department of Energy Strategic Petroleum Reserve (SPR) Program. Sandia National Laboratories, as the geotechnical advisor to the SPR, conducts site-characterization investigations and other longer-term geotechnical and engineering studies in support of the program. This report describes the conversion of two-dimensional geologic interpretations of the West Hackberry site into three-dimensional geologic models. The new models include the geometry of the salt dome, the surrounding sedimentary layers, mapped faults, and a portion of the oil storage caverns at the site. This work provides a realistic and internally consistent geologic model of the West Hackberry site that can be used in support of future work.

  2. A Mathematical Model of Collective Cell Migration in a Three-Dimensional, Heterogeneous Environment

    PubMed Central

    Stonko, David P.; Manning, Lathiena; Starz-Gaiano, Michelle; Peercy, Bradford E.

    2015-01-01

    Cell migration is essential in animal development, homeostasis, and disease progression, but many questions remain unanswered about how this process is controlled. While many kinds of individual cell movements have been characterized, less effort has been directed towards understanding how clusters of cells migrate collectively through heterogeneous, cellular environments. To explore this, we have focused on the migration of the border cells during Drosophila egg development. In this case, a cluster of different cell types coalesce and traverse as a group between large cells, called nurse cells, in the center of the egg chamber. We have developed a new model for this collective cell migration based on the forces of adhesion, repulsion, migration and stochastic fluctuation to generate the movement of discrete cells. We implement the model using Identical Math Cells, or IMCs. IMCs can each represent one biological cell of the system, or can be aggregated using increased adhesion forces to model the dynamics of larger biological cells. The domain of interest is filled with IMCs, each assigned specific biophysical properties to mimic a diversity of cell types. Using this system, we have successfully simulated the migration of the border cell cluster through an environment filled with larger cells, which represent nurse cells. Interestingly, our simulations suggest that the forces utilized in this model are sufficient to produce behaviors of the cluster that are observed in vivo, such as rotation. Our framework was developed to capture a heterogeneous cell population, and our implementation strategy allows for diverse, but precise, initial position specification over a three- dimensional domain. Therefore, we believe that this model will be useful for not only examining aspects of Drosophila oogenesis, but also for modeling other two or three-dimensional systems that have multiple cell types and where investigating the forces between cells is of interest. PMID:25875645

  3. The Coupling of Finite Element and Integral Equation Representations for Efficient Three-Dimensional Modeling of Electromagnetic Scattering and Radiation

    NASA Technical Reports Server (NTRS)

    Cwik, Tom; Zuffada, Cinzia; Jamnejad, Vahraz

    1996-01-01

    Finite element modeling has proven useful for accurtely simulating scattered or radiated fields from complex three-dimensional objects whose geometry varies on the scale of a fraction of a wavelength.

  4. Three-dimensional lake water quality modeling: sensitivity and uncertainty analyses.

    PubMed

    Missaghi, Shahram; Hondzo, Miki; Melching, Charles

    2013-11-01

    Two sensitivity and uncertainty analysis methods are applied to a three-dimensional coupled hydrodynamic-ecological model (ELCOM-CAEDYM) of a morphologically complex lake. The primary goals of the analyses are to increase confidence in the model predictions, identify influential model parameters, quantify the uncertainty of model prediction, and explore the spatial and temporal variabilities of model predictions. The influence of model parameters on four model-predicted variables (model output) and the contributions of each of the model-predicted variables to the total variations in model output are presented. The contributions of predicted water temperature, dissolved oxygen, total phosphorus, and algal biomass contributed 3, 13, 26, and 58% of total model output variance, respectively. The fraction of variance resulting from model parameter uncertainty was calculated by two methods and used for evaluation and ranking of the most influential model parameters. Nine out of the top 10 parameters identified by each method agreed, but their ranks were different. Spatial and temporal changes of model uncertainty were investigated and visualized. Model uncertainty appeared to be concentrated around specific water depths and dates that corresponded to significant storm events. The results suggest that spatial and temporal variations in the predicted water quality variables are sensitive to the hydrodynamics of physical perturbations such as those caused by stream inflows generated by storm events. The sensitivity and uncertainty analyses identified the mineralization of dissolved organic carbon, sediment phosphorus release rate, algal metabolic loss rate, internal phosphorus concentration, and phosphorus uptake rate as the most influential model parameters.

  5. A Semi-Implicit, Three-Dimensional Model for Estuarine Circulation

    USGS Publications Warehouse

    Smith, Peter E.

    2006-01-01

    A semi-implicit, finite-difference method for the numerical solution of the three-dimensional equations for circulation in estuaries is presented and tested. The method uses a three-time-level, leapfrog-trapezoidal scheme that is essentially second-order accurate in the spatial and temporal numerical approximations. The three-time-level scheme is shown to be preferred over a two-time-level scheme, especially for problems with strong nonlinearities. The stability of the semi-implicit scheme is free from any time-step limitation related to the terms describing vertical diffusion and the propagation of the surface gravity waves. The scheme does not rely on any form of vertical/horizontal mode-splitting to treat the vertical diffusion implicitly. At each time step, the numerical method uses a double-sweep method to transform a large number of small tridiagonal equation systems and then uses the preconditioned conjugate-gradient method to solve a single, large, five-diagonal equation system for the water surface elevation. The governing equations for the multi-level scheme are prepared in a conservative form by integrating them over the height of each horizontal layer. The layer-integrated volumetric transports replace velocities as the dependent variables so that the depth-integrated continuity equation that is used in the solution for the water surface elevation is linear. Volumetric transports are computed explicitly from the momentum equations. The resulting method is mass conservative, efficient, and numerically accurate.

  6. Geostatistical three-dimensional modeling of oolite shoals, St. Louis Limestone, southwest Kansas

    USGS Publications Warehouse

    Qi, L.; Carr, T.R.; Goldstein, R.H.

    2007-01-01

    In the Hugoton embayment of southwestern Kansas, reservoirs composed of relatively thin (<4 m; <13.1 ft) oolitic deposits within the St. Louis Limestone have produced more than 300 million bbl of oil. The geometry and distribution of oolitic deposits control the heterogeneity of the reservoirs, resulting in exploration challenges and relatively low recovery. Geostatistical three-dimensional (3-D) models were constructed to quantify the geometry and spatial distribution of oolitic reservoirs, and the continuity of flow units within Big Bow and Sand Arroyo Creek fields. Lithofacies in uncored wells were predicted from digital logs using a neural network. The tilting effect from the Laramide orogeny was removed to construct restored structural surfaces at the time of deposition. Well data and structural maps were integrated to build 3-D models of oolitic reservoirs using stochastic simulations with geometry data. Three-dimensional models provide insights into the distribution, the external and internal geometry of oolitic deposits, and the sedimentologic processes that generated reservoir intervals. The structural highs and general structural trend had a significant impact on the distribution and orientation of the oolitic complexes. The depositional pattern and connectivity analysis suggest an overall aggradation of shallow-marine deposits during pulses of relative sea level rise followed by deepening near the top of the St. Louis Limestone. Cemented oolitic deposits were modeled as barriers and baffles and tend to concentrate at the edge of oolitic complexes. Spatial distribution of porous oolitic deposits controls the internal geometry of rock properties. Integrated geostatistical modeling methods can be applicable to other complex carbonate or siliciclastic reservoirs in shallow-marine settings. Copyright ?? 2007. The American Association of Petroleum Geologists. All rights reserved.

  7. Three-dimensional geologic model of the southeastern Espanola Basin, Santa Fe County, New Mexico

    USGS Publications Warehouse

    Pantea, Michael P.; Hudson, Mark R.; Grauch, V.J.S.; Minor, Scott A.

    2011-01-01

    This multimedia model and report show and describe digital three-dimensional faulted surfaces and volumes of lithologic units that confine and constrain the basin-fill aquifers within the Espanola Basin of north-central New Mexico. These aquifers are the primary groundwater resource for the cities of Santa Fe and Espanola, six Pueblo nations, and the surrounding areas. The model presented in this report is a synthesis of geologic information that includes (1) aeromagnetic and gravity data and seismic cross sections; (2) lithologic descriptions, interpretations, and geophysical logs from selected drill holes; (3) geologic maps, geologic cross sections, and interpretations; and (4) mapped faults and interpreted faults from geophysical data. Modeled faults individually or collectively affect the continuity of the rocks that contain the basin aquifers; they also help define the form of this rift basin. Structure, trend, and dip data not previously published were added; these structures are derived from interpretations of geophysical information and recent field observations. Where possible, data were compared and validated and reflect the complex relations of structures in this part of the Rio Grande rift. This interactive geologic framework model can be used as a tool to visually explore and study geologic structures within the Espanola Basin, to show the connectivity of geologic units of high and low permeability between and across faults, and to show approximate dips of the lithologic units. The viewing software can be used to display other data and information, such as drill-hole data, within this geologic framework model in three-dimensional space.

  8. Modeling Primary Breakup: A Three-Dimensional Eulerian Level Set/Vortex Sheet Method for Two-Phase Interface Dynamics

    NASA Technical Reports Server (NTRS)

    Herrmann, M.

    2003-01-01

    This paper is divided into four parts. First, the level set/vortex sheet method for three-dimensional two-phase interface dynamics is presented. Second, the LSS model for the primary breakup of turbulent liquid jets and sheets is outlined and all terms requiring subgrid modeling are identified. Then, preliminary three-dimensional results of the level set/vortex sheet method are presented and discussed. Finally, conclusions are drawn and an outlook to future work is given.

  9. Wind-Tunnel Calibration and Correction Procedures for Three-Dimensional Models

    NASA Technical Reports Server (NTRS)

    Swanson, Robert S; Gillis, Clarence L

    1944-01-01

    Detailed methods are presented for determining the corrections to results from wind-tunnel tests of three-dimensional models for the effects of the model-support system, the nonuniform air flow in the tunnel, and the tunnel walls or jet boundaries. The procedures for determining the corrections are illustrated by equations and the required tests are discussed. Particular attention is given to the parts of the procedures dealing with drag measurements. Two general methods that are used for determining and applying the corrections to force tests are discussed. Some discussion is also included of the correction procedures to be used for wake survey tests. The methods described in this report apply only to tests at subcritical speeds. (author)

  10. Emergent O(n ) symmetry in a series of three-dimensional Potts models

    NASA Astrophysics Data System (ADS)

    Ding, Chengxiang; Blöte, Henk W. J.; Deng, Youjin

    2016-09-01

    We study the q -state Potts model on a simple cubic lattice with ferromagnetic interactions in one lattice direction, and antiferromagnetic interactions in the other two directions. As the temperature T decreases, the system undergoes a second-order phase transition that fits in the universality class of the three-dimensional O (n ) model with n =q -1 . This conclusion is based on the estimated critical exponents, and histograms of the order parameter. At even smaller T we find, for q =4 and 5, a first-order transition to a phase with a different type of long-range order. This long-range order dissolves at T =0 , and the system effectively reduces to a disordered two-dimensional Potts antiferromagnet. These results are obtained by means of Monte Carlo simulations and finite-size scaling.

  11. A sliding microtubule model incorporating axonemal twist and compatible with three-dimensional ciliary bending.

    PubMed

    Holwill, M E; Cohen, H J; Satir, P

    1979-02-01

    1. Equations are developed to calculate the relative displacements of the doublet microtubules at the tip of a cilium when the microtubules twist about the axis of the organelle. 2. Displacements measured from electron micrographs show asymmetry (or skew) which can be matched quantitatively by the theoretical model with the appropriate selection of twist angle and orientation of the axoneme with respect to the plane of beat. 3. For Elliptio cilia the experimental results are consistent with a planar effective stroke and a recovery stroke involving a three-dimensional bend. The plane of the effective stroke is not normal to a surface containing the central pair of microtubules but contains microtubule 2 to produce the observed skew. 4. This model for the beat also explains the range of orientations of axoneme observed in sections through the metachronal wave.

  12. Three-dimensional finite-element modeling of wave propagation in a transversely isotropic medium

    SciTech Connect

    Sun, Y.F.; Teng, Y.C.

    1994-12-31

    In this research, the authors present the numerical results of three-dimensional finite element modeling of elastic wave propagation in a half space of a transversely isotropic medium. The input physical parameters are taken from the physical model used by Chang and Gardner (1992). The synthetic seismograms of the three displacement components along the axis at an azimuth of 45{degree} to the fracture orientation on the surface are shown. Snapshots taken on the free surface are illustrated which are the displacement fields with polarization in the direction perpendicular to the fracture orientation. These snapshots show clearly the elliptical patterns demonstrating the effects of anisotropy on wave propagation. Four waves, namely, the fast and slow S-waves and the fast and slow P-waves, can be clearly observed.

  13. Three-dimensional Oldroyd-B fluid flow with Cattaneo-Christov heat flux model

    NASA Astrophysics Data System (ADS)

    Shehzad, S. A.; Hayat, T.; Abbasi, F. M.; Javed, Tariq; Kutbi, M. A.

    2016-04-01

    The impact of Cattaneo-Christov heat flux in three-dimensional flow of an Oldroyd-B fluid over a bidirectional stretching surface is explored in this article. The boundary layer flow of an incompressible fluid is considered. Heat transfer analysis is discussed via the Cattaneo-Christov model of heat flux. Similarity transformations lead to the nonlinear ordinary differential systems. Convergent solutions of dimensionless velocities and temperature have been computed. Convergence analysis is presented graphically and numerically. The influence of physical parameters on the velocities and temperature are plotted and discussed. We observed that the values of temperature gradient are higher for the Cattaneo-Christov heat flux model when we compare it with the values obtained by the simple Fourier's law of heat conduction.

  14. Three-Dimensional Cell Culture Models for Infectious Disease and Drug Development

    NASA Technical Reports Server (NTRS)

    Nickerson, Cheryl A.; Honer zu Bentrup, Kerstin; Ott, C. Mark

    2005-01-01

    Three-dimensional (3-D) cell cultures hold enormous potential to advance our understanding of infectious disease and to effectively translate basic cellular research into clinical applications. Using novel NASA bioreactor technology, the rotating wall vessel (RWV), we have engineered physiologically relevant 3-D human tissue culture models for infectious disease studies. The design of the RWV is based on the understanding that organs and tissues function in a 3-D environment, and that this 3-D architecture is critical for the differentiated form and function of tissues in vivo. The RWV provides large numbers of cells which are amenable to a wide variety of experimental manipulations and provides an easy, reproducible, and cost-effective approach to enhance differentiated features of cell culture models.

  15. Development and validation of a two-phase, three-dimensional model for PEM fuel cells.

    SciTech Connect

    Chen, Ken Shuang

    2010-04-01

    The objectives of this presentation are: (1) To develop and validate a two-phase, three-dimensional transport modelfor simulating PEM fuel cell performance under a wide range of operating conditions; (2) To apply the validated PEM fuel cell model to improve fundamental understanding of key phenomena involved and to identify rate-limiting steps and develop recommendations for improvements so as to accelerate the commercialization of fuel cell technology; (3) The validated PEMFC model can be employed to improve and optimize PEM fuel cell operation. Consequently, the project helps: (i) address the technical barriers on performance, cost, and durability; and (ii) achieve DOE's near-term technical targets on performance, cost, and durability in automotive and stationary applications.

  16. Three-dimensional spherical models of convection in the earth's mantle

    SciTech Connect

    Bercovici, D.; Schubert, G. ); Glatzmaier, G.A. )

    1989-05-26

    Three-dimensional, spherical models of mantle convection in the earth reveal that upwelling cylindrical plumes and downwelling planar sheets are the primary features of mantle circulation. Thus, subduction zones and descending sheetlike slabs in the mantle are fundamental characteristics of thermal convection in a spherical shell and are not merely the consequences of the rigidity of the slabs, which are cooler than the surrounding mantle. Cylindrical mantle plumes that cause hotspots such as Hawaii are probably the only form of active upwelling and are therefore not just secondary convective currents separate from the large-scale mantle circulation. Active sheetlike upwellings that could be associated with mid-ocean ridges did not develop in the model simulations, a result that is in agreement with evidence suggesting that ridges are passive phenomena resulting from the tearing of surface plates by the pull of descending slabs. 36 refs., 3 figs.

  17. Three phases in the three-dimensional Abelian-Higgs model with nonlocal gauge interactions

    SciTech Connect

    Takashima, Shunsuke; Ichinose, Ikuo; Matsui, Tetsuo; Sakakibara, Kazuhiko

    2006-08-15

    We study the phase structure of the three-dimensional (3D) nonlocal compact U(1) lattice gauge theory coupled with a Higgs field by Monte Carlo simulations. The nonlocal interactions among gauge variables are along the temporal direction and mimic the effect of local coupling to massless particles. In contrast to the 3D local Abelian-Higgs model having only the confinement phase, the present model exhibits the confinement, Higgs, and Coulomb phases separated by three second-order transition lines emanating from a triple point. This result is relevant not only to the 3D massless QED coupled with a Higgs field but also to electron fractionalization phenomena in strongly correlated electron systems like the high-T{sub c} superconductors and the fractional quantum Hall effect.

  18. Estimation of muscle response using three-dimensional musculoskeletal models before impact situation: a simulation study.

    PubMed

    Bae, Tae Soo; Loan, Peter; Choi, Kuiwon; Hong, Daehie; Mun, Mu Seong

    2010-12-01

    When car crash experiments are performed using cadavers or dummies, the active muscles' reaction on crash situations cannot be observed. The aim of this study is to estimate muscles' response of the major muscle groups using three-dimensional musculoskeletal model by dynamic simulations of low-speed sled-impact. The three-dimensional musculoskeletal models of eight subjects were developed, including 241 degrees of freedom and 86 muscles. The muscle parameters considering limb lengths and the force-generating properties of the muscles were redefined by optimization to fit for each subject. Kinematic data and external forces measured by motion tracking system and dynamometer were then input as boundary conditions. Through a least-squares optimization algorithm, active muscles' responses were calculated during inverse dynamic analysis tracking the motion of each subject. Electromyography for major muscles at elbow, knee, and ankle joints was measured to validate each model. For low-speed sled-impact crash, experiment and simulation with optimized and unoptimized muscle parameters were performed at 9.4 m/h and 10 m/h and muscle activities were compared among them. The muscle activities with optimized parameters were closer to experimental measurements than the results without optimization. In addition, the extensor muscle activities at knee, ankle, and elbow joint were found considerably at impact time, unlike previous studies using cadaver or dummies. This study demonstrated the need to optimize the muscle parameters to predict impact situation correctly in computational studies using musculoskeletal models. And to improve accuracy of analysis for car crash injury using humanlike dummies, muscle reflex function, major extensor muscles' response at elbow, knee, and ankle joints, should be considered.

  19. Slab1.0: A three-dimensional model of global subduction zone geometries

    USGS Publications Warehouse

    Hayes, G.P.; Wald, D.J.; Johnson, R.L.

    2012-01-01

    We describe and present a new model of global subduction zone geometries, called Slab1.0. An extension of previous efforts to constrain the two-dimensional non-planar geometry of subduction zones around the focus of large earthquakes, Slab1.0 describes the detailed, non-planar, three-dimensional geometry of approximately 85% of subduction zones worldwide. While the model focuses on the detailed form of each slab from their trenches through the seismogenic zone, where it combines data sets from active source and passive seismology, it also continues to the limits of their seismic extent in the upper-mid mantle, providing a uniform approach to the definition of the entire seismically active slab geometry. Examples are shown for two well-constrained global locations; models for many other regions are available and can be freely downloaded in several formats from our new Slab1.0 website, http://on.doi.gov/ d9ARbS. We describe improvements in our two-dimensional geometry constraint inversion, including the use of average active source seismic data profiles in the shallow trench regions where data are otherwise lacking, derived from the interpolation between other active source seismic data along-strike in the same subduction zone. We include several analyses of the uncertainty and robustness of our three-dimensional interpolation methods. In addition, we use the filtered, subduction-related earthquake data sets compiled to build Slab1.0 in a reassessment of previous analyses of the deep limit of the thrust interface seismogenic zone for all subduction zones included in our global model thus far, concluding that the width of these seismogenic zones is on average 30% larger than previous studies have suggested. Copyright 2011 by the American Geophysical Union.

  20. Modeling RedOx-based magnetohydrodynamics in three-dimensional microfluidic channels

    NASA Astrophysics Data System (ADS)

    Kabbani, Hussameddine; Wang, Aihua; Luo, Xiaobing; Qian, Shizhi

    2007-08-01

    RedOx-based magnetohydrodynamic (MHD) flows in three-dimensional microfluidic channels are investigated theoretically with a coupled mathematical model consisting of the Nernst-Planck equations for the concentrations of ionic species, the local electroneutrality condition for the electric potential, and the Navier-Stokes equations for the flow field. A potential difference is externally applied across two planar electrodes positioned along the opposing walls of a microchannel that is filled with a dilute RedOx electrolyte solution, and a Faradaic current transmitted through the solution results. The entire device is positioned under a magnetic field which can be provided by either a permanent magnet or an electromagnet. The interaction between the current density and the magnetic field induces Lorentz forces, which can be used to pump and/or stir fluids for microfluidic applications. The induced currents and flow rates in three-dimensional (3D) planar channels obtained from the full 3D model are compared with the experimental data obtained from the literature and those obtained from our previous two-dimensional mathematical model. A closed form approximation for the average velocity (flow rate) in 3D planar microchannels is derived and validated by comparing its predictions with the results obtained from the full 3D model and the experimental data obtained from the literature. The closed form approximation can be used to optimize the dimensions of the channel and to determine the magnitudes and polarities of the prescribed currents in MHD networks so as to achieve the desired flow patterns and flow rates.

  1. Petroleum migration pathways and charge concentration: A three-dimensional model

    SciTech Connect

    Hindle, A.D.

    1997-09-01

    Petroleum migration pathways through a basin are determined by the three-dimensional distribution of discontinuous sealing surfaces, which are usually parallel to bedding. The petroleum migrates below the sealing surface, taking the structurally most advantageous route. The three-dimensional distribution of migration pathways within the petroleum system can be modeled on a personal computer using a program based on the parameters discussed in this paper. Application of the model to the Paris and Williston basins demonstrates that a good correlation between predicted pathways and discovered accumulations can be made using simple models. Pathways form a dense network overlying generating areas in the central parts of basins. Toward the basin margins these routes commonly become increasingly focused into discrete pathways by the sealing-surface morphologies. Eventually, these pathways may reach the surface as seepages. It is important to integrate surface outcrops of migration routes (surface seepages) into migration modeling. Deflection of the pathways from the structurally most advantageous route below the sealing surface may be caused by lateral sealing barriers due to faces variation in the carrier rock below the seal, fault juxtaposition, or cross-formational seals such as salt intrusions. Deflection of pathways also occurs where there are hydrodynamic conditions in response to topography-driven groundwater flow. Zones of vertical migration are associated with facies changes along the horizon of the sealing surface into a nonsealing facies, or juxtaposition to nonsealing strata by faults. Vertical migration from either normally or abnormally pressured strata is most likely to occur into normally or lesser pressured strata at intrabasinal highs where hydrocarbons can be stored and transferred at times of temporary seal rupture.

  2. Vortical flow in human elbow joints: a three-dimensional computed tomography modeling study.

    PubMed

    Adikrishna, Arnold; Kekatpure, Aashay L; Tan, Jun; Lee, Hyun-Joo; Deslivia, Maria Florencia; Jeon, In-Ho

    2014-10-01

    The human elbow joint has been regarded as a loose hinge joint, with a unique helical motion of the axis during extension-flexion. This study was designed to identify the helical axis in the ulnohumeral joint during elbow extension-flexion by tracking the midpoint between the coronoid tip and the olecranon tip of the proximal ulna in a three-dimensional (3D) computed tomography (CT) image model. The elbows of four volunteers were CT-scanned at four flexion angles (0°, 45°, 90°, and 130°) at neutral rotation with a custom-made holding device to control any motion during scanning. Three-dimensional models of each elbow were reconstructed and a 3D ulnohumeral joint at 45°, 90°, and 130° was superimposed onto a fully extended joint (0°) by rotating and translating each 3D ulnohumeral joint along the axes. The midpoints of the olecranon and coronoid tips were interpolated using cubic spline technique and the dynamic elbow motion was plotted to determine the motion of the helical axis. The means and standard deviations were subsequently calculated. The average midpoint pattern of joint motion from extension to flexion was elliptical-orbit-like when projected onto a sagittal plane and continuously translated a mean 2.14 ± 0.34 mm (range, 1.83-2.52 mm) to the lateral side during elbow extension-flexion. In 3D space, the average midpoint pattern of the ulnohumeral joint resembles a vortical flow, spinning along an imaginary axis, with an inconsistent radius from 0° to 130° flexion. The ulnohumeral joint axis both rotates and translates during elbow extension-flexion, with a vortex-flow motion occurring during flexion in 3D model analysis. This motion should be considered when performing hinged external fixation, total elbow replacement and medial collateral ligament reconstruction surgery.

  3. Structure and modeling of the three dimensional boundary layer on a rotating disk. Final report

    SciTech Connect

    Eaton, J.K.

    1996-12-01

    Almost all practical turbulent flows include three dimensional boundary layers (3DTBL`s), and in many cases, the 3DTBL is the dominant feature of the flow. A boundary layer is defined as a thin layer adjacent to the surface in which the velocity drops rapidly from the freestream value to zero at the wall. A 3D boundary layer is one in which the flow direction also changes rapidly approaching the wall. This change in the flow direction called skewing is caused by transverse pressure gradients, centrifugal forces, or motion of the surface. Most research on turbulent boundary layers has been done in simple two dimensional flows in carefully controlled wind tunnels. Such boundary layers are now well understood, and excellent models are available describing both the fluid mechanics and heat transfer behavior. Recent fluid mechanics studies have shown that skewing can have a pronounced effect on the boundary layer turbulence. Models based on eddy-viscosity concepts fail, and more complex stress transport models cannot capture the reduction of turbulent mixing that usually accompanies skewing. It was unknown prior to the present study what effect the skewing might have on turbulent heat transfer. It was suspected that turbulent heat transport would be reduced in analogy to the reductions of turbulent shear stress. It was also unknown how the skewing would effect the turbulent Prandtl number, a quantity which is embedded in most turbulent heat transfer prediction schemes. The objectives of the present study were then to study the surface heat transfer rate and the turbulent heat flux in a simple three dimensional boundary layer. In particular, the research addressed the heat transfer from a heated disk rotating in an otherwise quiescent environment.

  4. Three-Dimensional Soil Landscape Modeling: A Potential Earth Science Teaching Tool

    ERIC Educational Resources Information Center

    Schmid, Brian M.; Manu, Andrew; Norton, Amy E.

    2009-01-01

    Three-dimensional visualization is helpful in understanding soils, and three dimensional (3-D) tools are gaining popularity in teaching earth sciences. Those tools are still somewhat underused in soil science, yet soil properties such as texture, color, and organic carbon content vary both vertically and horizontally across the landscape. These…

  5. Which animal model for understanding human navigation in a three-dimensional world?

    PubMed

    Orban, Guy A

    2013-10-01

    Single-cell studies of monkey posterior parietal cortex (PPC) have revealed the extensive neuronal representations of three-dimensional subject motion and three-dimensional layout of the environment. I propose that navigational planning integrates this PPC information, including gravity signals, with horizontal-plane based information provided by the hippocampal formation, modified in primates by expansion of the ventral stream.

  6. Simulation of dilute polymeric fluids in a three-dimensional contraction using a multiscale FENE model

    SciTech Connect

    Griebel, M. E-mail: ruettgers@ins.uni-bonn.de; Rüttgers, A. E-mail: ruettgers@ins.uni-bonn.de

    2014-05-15

    The multiscale FENE model is applied to a 3D square-square contraction flow problem. For this purpose, the stochastic Brownian configuration field method (BCF) has been coupled with our fully parallelized three-dimensional Navier-Stokes solver NaSt3DGPF. The robustness of the BCF method enables the numerical simulation of high Deborah number flows for which most macroscopic methods suffer from stability issues. The results of our simulations are compared with that of experimental measurements from literature and show a very good agreement. In particular, flow phenomena such as a strong vortex enhancement, streamline divergence and a flow inversion for highly elastic flows are reproduced. Due to their computational complexity, our simulations require massively parallel computations. Using a domain decomposition approach with MPI, the implementation achieves excellent scale-up results for up to 128 processors.

  7. Three-dimensional temperature effect modelling of piezoceramic transducers used for Lamb wave based damage detection

    NASA Astrophysics Data System (ADS)

    Kijanka, Piotr; Packo, Pawel; Zhu, Xuan; Staszewski, Wieslaw J.; Lanza di Scalea, Francesco

    2015-06-01

    The paper presents a three-dimensional temperature-dependent model of surface-bonded, low-profile piezoceramic transducers (PZT) used for Lamb wave propagation. The effect of temperature on Lamb wave actuation, propagation and sensing is investigated. The major focus is on the study of actuation and sensing properties of PZT for various temperature levels. These properties are investigated through the electric field analysis of transducers. The temperature effect on transducer bond layers is also investigated. Numerically simulated amplitude responses are analysed for various temperatures and excitation frequencies. Numerical simulations are validated experimentally. The results demonstrate that temperature-dependent physical properties of PZT, bond layers and particularly host structures significantly affect the amplitude and phase of Lamb wave responses.

  8. Global climate changes as forecast by Goddard Institute for Space Studies three-dimensional model

    NASA Technical Reports Server (NTRS)

    Hansen, J.; Fung, I.; Lacis, A.; Rind, D.; Lebedeff, S.; Ruedy, R.; Russell, G.

    1988-01-01

    The global climate effects of time-dependent atmospheric trace gas and aerosol variations are simulated by NASA-Goddard's three-dimensional climate model II, which possesses 8 x 10-deg horizontal resolution, for the cases of a 100-year control run and three different atmospheric composition scenarios in which trace gas growth is respectively a continuation of current exponential trends, a reduced linear growth, and a rapid curtailment of emissions due to which net climate forcing no longer increases after the year 2000. The experiments begin in 1958, run to the present, and encompass measured or estimated changes in CO2, CH4, N2O, chlorofluorocarbons, and stratospheric aerosols. It is shown that the greenhouse warming effect may be clearly identifiable in the 1990s.

  9. Segmentation of Three Dimensional Cell Culture Models from aSingle Focal Plane

    SciTech Connect

    Chang, Hang; Parvin, Bahram

    2006-11-01

    Three dimensional cell culture models offer new opportunities for development of computational techniques for segmentation and localization. These assays have a unique signature of a clump of cells that correspond to a functioning colony. Often the nuclear compartment is labeled and then imaged with fluorescent microscopy to provide context for protein localization. These colonies are first delineated from background using the level set method. Within each colony, nuclear regions are then bounded by their center of mass through radial voting, and a local neighborhood for each nucleus is established through Voronoi tessellation. Finally, the level set method is applied again within each Voronoi region to delineate the nuclear compartment. The paper concludes with the application of the proposed method to a dataset of experimental data demonstrating a stable solution when iterative radial voting and level set methods are used synergistically.

  10. Periodic standing-wave approximation: Overview and three-dimensional scalar models

    SciTech Connect

    Andrade, Zeferino; Beetle, Christopher; Blinov, Alexey; Bromley, Benjamin; Burko, Lior M.; Cranor, Maria; Price, Richard H.; Owen, Robert

    2004-09-15

    The periodic standing-wave method for binary inspiral computes the exact numerical solution for periodic binary motion with standing gravitational waves, and uses it as an approximation to slow binary inspiral with outgoing waves. Important features of this method presented here are: (i) the mathematical nature of the 'mixed' partial differential equations to be solved (ii) the meaning of standing waves in the method (iii) computational difficulties, and (iv) the 'effective linearity' that ultimately justifies the approximation. The method is applied to three-dimensional nonlinear scalar model problems, and the numerical results are used to demonstrate extraction of the outgoing solution from the standing-wave solution, and the role of effective linearity.

  11. A three-dimensional turbulent compressible flow model for ejector and fluted mixers

    NASA Technical Reports Server (NTRS)

    Rushmore, W. L.; Zelazny, S. W.

    1978-01-01

    A three dimensional finite element computer code was developed to analyze ejector and axisymmetric fluted mixer systems whose flow fields are not significantly influenced by streamwise diffusion effects. A two equation turbulence model was used to make comparisons between theory and data for various flow fields which are components of the ejector system, i.e., (1) turbulent boundary layer in a duct; (2) rectangular nozzle (free jet); (3) axisymmetric nozzle (free jet); (4) hypermixing nozzle (free jet); and (5) plane wall jet. Likewise, comparisons of the code with analytical results and/or other numerical solutions were made for components of the axisymmetric fluted mixer system. These included: (1) developing pipe flow; (2) developing flow in an annular pipe; (3) developing flow in an axisymmetric pipe with conical center body and no fluting and (4) developing fluted pipe flow. Finally, two demonstration cases are presented which show the code's ability to analyze both the ejector and axisymmetric fluted mixers.

  12. Three-Dimensional Model of the Scatterer Distribution in Cirrhotic Liver

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Tadashi; Nakamura, Keigo; Hachiya, Hiroyuki

    2003-05-01

    Ultrasonic B-mode images are affected by changes in scatterer distribution. It is hard to estimate the relationship between the ultrasonic image and the tissue structure quantitatively because we cannot observe the continuous stages of liver cirrhosis tissue clinically, particularly the beginning stage. In this paper, we propose a three-dimensional modeling method of scatterer distribution for normal and cirrhotic livers to confirm the influence of the change in the form of scatterer distribution on echo information. The algorithm of the method includes parameters which determine the expansion of nodules and fibers. Using the B-mode images which are obtained from these scatterer distributions, we analyze the relationship between the changes in the form of biological tissue and the changes in the B-mode images during progressive liver cirrhosis.

  13. Analytical modeling and three-dimensional finite element simulation of line edge roughness in scatterometry.

    PubMed

    Kato, Akiko; Burger, Sven; Scholze, Frank

    2012-09-20

    The influence of edge roughness in angle-resolved scatterometry at periodically structured surfaces is investigated. A good description of the radiation interaction with structured surfaces is crucial for the understanding of optical imaging processes such as, e.g., in photolithography. We compared an analytical two-dimensional (2D) model and a numerical three-dimensional simulation with respect to the characterization of 2D diffraction of a line grating involving structure roughness. The results show a remarkably high agreement. The diffraction intensities of a rough structure can therefore be estimated using the numerical simulation result of an undisturbed structure and an analytically derived correction function. This work allows to improve scatterometric results for the case of practically relevant 2D structures. PMID:23033013

  14. Three-Dimensional Modelling inside a Differential Pressure Laminar Flow Bioreactor Filled with Porous Media.

    PubMed

    Weyand, Birgit; Israelowitz, Meir; Kramer, James; Bodmer, Christian; Noehre, Mariel; Strauss, Sarah; Schmälzlin, Elmar; Gille, Christoph; von Schroeder, Herbert P; Reimers, Kerstin; Vogt, Peter M

    2015-01-01

    A three-dimensional computational fluid dynamics- (CFD-) model based on a differential pressure laminar flow bioreactor prototype was developed to further examine performance under changing culture conditions. Cell growth inside scaffolds was simulated by decreasing intrinsic permeability values and led to pressure build-up in the upper culture chamber. Pressure release by an integrated bypass system allowed continuation of culture. The specific shape of the bioreactor culture vessel supported a homogenous flow profile and mass flux at the scaffold level at various scaffold permeabilities. Experimental data showed an increase in oxygen concentration measured inside a collagen scaffold seeded with human mesenchymal stem cells when cultured in the perfusion bioreactor after 24 h compared to static culture in a Petri dish (dynamic: 11% O2 versus static: 3% O2). Computational fluid simulation can support design of bioreactor systems for tissue engineering application.

  15. Three-dimensional numerical simulation of a bird model in unsteady flight

    NASA Astrophysics Data System (ADS)

    Lin-Lin, Zhu; Hui, Guan; Chui-Jie, Wu

    2016-07-01

    In this paper, a type of numerical simulation of a three-dimensional (3D) bionic bird with flapping wings in a viscous flow is studied. The model is a self-propelled flying bird capable of free rotation and translation whose flying motion follows the laws of conservation of momentum and angular momentum. The bird is propelled and lifted through flapping and rotating wings and most of thrust force and lift force are exerted on both wings. Both the vortex structures and the flight characteristics are also presented. The relationship between both wings' movement and the vortex structures as well as that between both wings' movement and flight characteristics are also analyzed in this paper. The study uses a 3D computational fluid dynamics package that includes the combined immersed boundary method, volume of fluid method, adaptive multigrid finite volume method, and control strategy for swimming and flying.

  16. Three-dimensional organotypic culture: experimental models of mammalian biology and disease

    PubMed Central

    Shamir, Eliah R.; Ewald, Andrew J.

    2015-01-01

    Mammalian organs are challenging to study as they are fairly inaccessible to experimental manipulation and optical observation. Recent advances in three-dimensional (3D) culture techniques, coupled with the ability to independently manipulate genetic and microenvironmental factors, have enabled the real-time study of mammalian tissues. These systems have been used to visualize the cellular basis of epithelial morphogenesis, to test the roles of specific genes in regulating cell behaviours within epithelial tissues and to elucidate the contribution of microenvironmental factors to normal and disease processes. Collectively, these novel models can be used to answer fundamental biological questions and generate replacement human tissues, and they enable testing of novel therapeutic approaches, often using patient-derived cells. PMID:25237826

  17. Conversion of the Bayou Choctaw geological site characterization report to a three-dimensional model.

    SciTech Connect

    Stein, Joshua S.; Rautman, Christopher Arthur

    2004-02-01

    The geologic model implicit in the original site characterization report for the Bayou Choctaw Strategic Petroleum Reserve Site near Baton Rouge, Louisiana, has been converted to a numerical, computer-based three-dimensional model. The original site characterization model was successfully converted with minimal modifications and use of new information. The geometries of the salt diapir, selected adjacent sedimentary horizons, and a number of faults have been modeled. Models of a partial set of the several storage caverns that have been solution-mined within the salt mass are also included. Collectively, the converted model appears to be a relatively realistic representation of the geology of the Bayou Choctaw site as known from existing data. A small number of geometric inconsistencies and other problems inherent in 2-D vs. 3-D modeling have been noted. Most of the major inconsistencies involve faults inferred from drill hole data only. Modem computer software allows visualization of the resulting site model and its component submodels with a degree of detail and flexibility that was not possible with conventional, two-dimensional and paper-based geologic maps and cross sections. The enhanced visualizations may be of particular value in conveying geologic concepts involved in the Bayou Choctaw Strategic Petroleum Reserve site to a lay audience. A Microsoft WindowsTM PC-based viewer and user-manipulable model files illustrating selected features of the converted model are included in this report.

  18. Three-dimensional detailed numerical model of a field-scale rotary kiln incinerator

    SciTech Connect

    Leger, C.B.; Cundy, V.A.; Sterling, A.M. )

    1993-04-01

    A detailed three-dimensional numerical model of baseline (support burners only) operation in a rotary kiln incinerator is presented. The focus of this model is on gas-phase fluid mechanics, neglecting solid waste combustion and radiative heat transfer. The model is compared to experimental data, and although relatively crude, it demonstrates remarkably good qualitative and quantitative predictive capability. The model demonstrates that thermal buoyancy is the cause of observed vertical stratification near the exit of the modeled kiln. The model also suggests that the addition of turbulence mixing air actually increases the degree of stratification rather than augmenting mixing, as had been previously suggested. Elucidating the mechanism by which this occurs has resulted in a reinterpretation of the experimental data. The model also suggests that there is probably a zone of recirculation across the kiln exit plane. A parametric study using the model shows that the location and quantity of leak air into the kiln have a major influence on the flow inside the kiln. The study suggests that preheating turbulence air may have little effect on gas-phase mixing. Overall, this modeling study has demonstrated that a relatively simple numerical model of a rotary kiln incinerator can provide valuable insight into the process, especially when used in conjunction with experimental data. 21 refs., 17 figs., 3 tabs.

  19. Three-dimensional resistivity modeling of GREATEM survey data from Ontake Volcano, northwest Japan

    NASA Astrophysics Data System (ADS)

    Abd Allah, Sabry; Mogi, Toru

    2016-05-01

    Ontake Volcano is located in central Japan, 200 km northwest of Tokyo and erupted on September 27, 2014. To study the structure of Ontake Volcano and discuss the process of its phreatic eruption, which can help in future eruptions mitigation, airborne electromagnetic (AEM) surveys using the grounded electrical-source airborne transient electromagnetic (GREATEM) system were conducted over Ontake Volcano. Field measurements and data analysis were done by OYO Company under the Sabo project managed by the Ministry of Land, Infrastructure, Transport and Tourism. Processed data and 1D resistivity models were provided by this project. We performed numerical forward modeling to generate a three-dimensional (3D) resistivity structure model that fits the GREATEM data where a composite of 1D resistivity models was used as the starting model. A 3D electromagnetic forward-modeling scheme based on a staggered-grid finite-difference method was modified and used to calculate the response of the 3D resistivity model along each survey line. We verified the model by examining the fit of magnetic-transient responses between the field data and 3D forward-model computed data. The preferred 3D resistivity models show that a moderately resistive structure (30-200 Ω m) is characteristic of most of the volcano, and were able to delineate a hydrothermal zone within the volcanic edifice. This hydrothermal zone may be caused by a previous large sector collapse.

  20. Three-Dimensional Numerical Modeling of Free-Burning Arcs Using a CFD-MHD Coupled Method

    NASA Astrophysics Data System (ADS)

    Lee, Jong-Chul; Lee, Won-Ho; Kim, Youn-Jea

    2015-09-01

    Because a scientific understanding of the thermal behavior of arcs and their electrodes in free-burning arc systems is very important for improving industrial applications, numerous theoretical and experimental papers have been published in the last decade. However, the flow patterns inside the free-burning arc system must be of the 3-D feature, and 2-D modeling cannot help in predicting the 3-D flow and heat transfer within the system. This paper is concerned with developing a capability to model free-burning high-intensity argon arcs (self-consistent model) and enhancing the accuracy of numerical results according to three-dimensional calculations. It was found that the computed temperatures along the axis between the cathode tip and the anode surface show good agreement with two different measured data. Although the LTE model can reasonably predict the overall arc voltage for free-burning arcs, it fails to account accurately what happens at the near electrode region. An accurate solution near electrodes has to be based on non-LTE model to ensure current continuation in the low temperature region. Calculation of the energy flux towards the anode also requires the mechanisms operating in the non-LTE situation be taken into account in the model.

  1. A two- and three-dimensional numerical modelling benchmark of slab detachment

    NASA Astrophysics Data System (ADS)

    Thieulot, Cedric; Glerum, Anne; Hillebrand, Bram; Schmalholz, Stefan; Spakman, Wim; Torsvik, Trond

    2014-05-01

    Subduction is likely to be the most studied phenomenon in Numerical Geodynamics. Over the past 20 years, hundreds of publications have focused on its various aspects (influence of the rheology and thermal state of the plates, slab-mantle coupling, roll-back, mantle wedge evolution, buoyancy changes due to phase change, ...) and results were obtained with a variety of codes. Slab detachment has recently received some attention (e.g. Duretz, 2012) but remains a field worth exploring due to its profound influence on dynamic topography, mantle flow and subsequent stress state of the plates, and is believed to have occured in the Zagros, Carpathians and beneath eastern Anatolia, to name only a few regions. Following the work of Schmalholz (2011), we propose a two- and three-dimensional numerical benchmark of slab detachment. The geometry is simple: a power-law T-shaped plate including an already subducted slab overlies the mantle whose viscosity is either linear or power-law. Boundary conditions are free-slip on the top and the bottom of the domain, and no-slip on the sides. When the system evolves in time, the slab stretches out vertically and shows buoyancy-driven necking, until it finally detaches. The benchmark is subdivided into several sub-experiments with gradually increase in complexity (free surface, coupling of the rheology with temperature, ...). An array of objective measurements is recorded throughout the simulation such as the width of the necked slab over time and the exact time of detachment. The experiments will be run in two-dimensions and repeated in three-dimensional, the latter case being designed so as to allow both poloidal and toroidal flow. We show results obtained with a multitude of Finite Element and Finite Difference codes, using either compositional fields, level sets or tracers to track the compositions. A good agreement is found for most of the measurements in the two-dimensional case, and preliminary three-dimensional measurements will

  2. Preliminary three-dimensional discrete fracture model, Tiva Canyon tuff, Yucca Mountain area, Nye County, Nevada

    SciTech Connect

    Anna, L.O.

    1998-09-01

    A three-dimensional discrete fracture model was completed to investigate the potential effects of fractures on the flow of water at Yucca Mountain, Nye County, Nevada. A fracture network of the Exploratory Studies Facility starter tunnel area was simulated and calibrated with field data. Two modeled volumes were used to simulate three-dimensional fracture networks of the Tiva Canyon tuff. One volume had a width and length of 150 meters, and the other had a width and length of 200 meters; both volumes were 60 meters thick. The analysis shows that the fracture system in the Exploratory Studies Facility starter tunnel area has numerous connected fractures that have relatively large permeabilities. However, pathway analysis between three radial boreholes indicated there were few pathways and little connection, which is consistent with results of cross-boreholes pressure testing. Pathway analysis also showed that at the scales used there was only one pathway connecting one end of the flow box to the opposite end. The usual vertical pathway was along one large fracture, whereas in four horizontal directions the pathway was from multiple fracture connections. As a result, the fracture network can be considered sparse. The fracture network was refined by eliminating nonconductive fractures determined from field-derived permeabilities. Small fractures were truncated from the simulated network without any effect on the overall connectivity. Fractures as long as 1.25 meters were eliminated (a large percentage of the total number of fractures) from the network without altering the number of pathways. Five directional permeabilities were computed for the 150- and 200-meter-scale flow box areas. Permeabilities for the 150-meter scale vary by almost two orders of magnitude, with the principal permeability direction being easterly. At the 200-meter scale, however, the flow box permeabilities only vary by a factor of four, with the principal permeability direction being vertical.

  3. Three-dimensional modelling of water flow through a heterogeneous vadose zone

    NASA Astrophysics Data System (ADS)

    Angulo-Jaramillo, R.; Cazalets, H.; Goutaland, D.; Winiarski, T.; Delolme, C.

    2007-12-01

    Stormwater infiltration basins have become a common alternative practice to traditional stormwater pipe networks in urban areas. They are often built in permeable subsurface soils, such as alluvial deposits. These sedimentary deposits are highly heterogeneous which generate preferential flow paths that may cause non- uniform transport of contaminants at great depths. Thus, the hypothesis of using homogeneous deposit cannot be considered valid at the scale of infiltration basin. Therefore, it is required a fine scale three-dimensional numerical simulations of fluid flow and solute transport to understand how subsurface heterogeneities affect fluid flow and contaminant transfer. The aim of our study is to improve the understanding of the water flow mechanisms occurring at the lithofacies scale in the heterogeneous vadose zone of infiltration basin. The studied basin, located in the eastern suburbs of Lyon (France), is built in quaternary glaciofluvial deposits. Results from previous studies show that the glaciofluvial deposit is composed of 4 main lithofacies: sands, bimodal sandy gravels, heterometric sandy gravels, and openframework gravels. These lithofacies are organized in braided river deposits architecture. Ground-Penetrating Radar was assessed to characterize the structural units of the studied deposits. Hydraulic properties of each lithofacies were characterized on analogous modern glaciofluvial lithofacies, leading to the definition of hydrofacies. Geophysical measurements (Ground-Penetrating Radar and Electrical Resistivity) performed on a limited zone of the basin was interpreted to define a lithofacies distribution. Hydrofacies properties were used to build a three- dimensional hydrostratigraphic model of the glaciofluvial deposit. This model was implemented in the finite element program Hydrus3D. The results show that openframework gravels cause capillary barrier effects leading to funneled flows, i.e. non- vertical water flows along lithofacies

  4. Three dimensional observations and modelling of intergranular stress corrosion cracking in austenitic stainless steel

    NASA Astrophysics Data System (ADS)

    Marrow, T. J.; Babout, L.; Jivkov, A. P.; Wood, P.; Engelberg, D.; Stevens, N.; Withers, P. J.; Newman, R. C.

    2006-06-01

    Stress corrosion cracking is a life-limiting factor in many components of nuclear power plant in which failure of structural components presents a substantial hazard to both safety and economic performance. Uncertainties in the kinetics of short crack behaviour can have a strong influence on lifetime prediction, and arise due both to the complexity of the underlying mechanisms and to the difficulties of making experimental observations. This paper reports on an on-going research programme into the dynamics and morphology of intergranular stress corrosion cracking in austenitic stainless steels in simulated light water environments, which makes use of recent advances in high resolution X-ray microtomography. In particular in situ, three dimensional X-ray tomographic images of intergranular stress corrosion crack nucleation and growth in sensitised austenitic stainless steel provide evidence for the development of crack bridging ligaments, caused by the resistance of non-sensitised special grain boundaries. In parallel a simple grain bridging model, introduced to quantify the effect of crack bridging on crack development, has been assessed for thermo-mechanically processed microstructures via statically loaded room temperature simulant solution tests and as well as high temperature/pressure autoclave studies. Thermo-mechanical treatments have been used to modify the grain size, grain boundary character and triple junction distributions, with a consequent effect on crack behaviour. Preliminary three-dimensional finite element models of intergranular crack propagation have been developed, with the aim of investigating the development of crack bridging and its effects on crack propagation and crack coalescence.

  5. The sensing and display of three-dimensional information with emphasis on solid modelling: Status and applications

    NASA Astrophysics Data System (ADS)

    Gerhardt, L. A.

    1985-09-01

    The sensing of three dimensional information is addressed, the display/representation of three dimensional information is considered. With respect to the sensing of three dimensional information, a variety of approaches are discussed including the use of structured light, the use of displaced sensors to develop stereo pairs, and coherence processing and time of flight measurement. Other techniques described are interpretation of object motion as a measurement of depth perception, and general methods for utilizing depth of field. The advantages and disadvantages of each are discussed and comparisons made. Three dimensional display techniques is also discussed. The appraoches covered include graphics, stereo pairs, holograms, vibrating mirrors, and other optical systems. Applications are reviewed with examples of results such as the use of vibrating mirror technology for the three dimensional display of compterized tomography. Solid modelling as an approach to the display and representation of three dimensional information is reviewed. Following a definition of solid modelling, the advantages of this generic approach are reviewed and analyzed. The relationship of solid modelling to robotics and artificial intelligence is made, and trends cited with respect to hardware costs, portability of software, computational efficiency, display resolution, and neutral data bases. The paper concludes by giving examples of some of the key applications of solid modelling in the automative industry, aircraft industry and CAM, among others.

  6. Precise determination of the critical percolation threshold for the three-dimensional ``Swiss cheese'' model using a growth algorithm

    NASA Astrophysics Data System (ADS)

    Lorenz, Christian D.; Ziff, Robert M.

    2001-02-01

    Precise values for the critical threshold for the three-dimensional "Swiss cheese" continuum percolation model have been calculated using extensive Monte Carlo simulations. These simulations used a growth algorithm and memory blocking scheme similar to what we used previously in three-dimensional lattice percolation. The simulations yield a value for the critical number density nc=0.652 960±0.000 005, which confirms recent work but extends the precision by two significant figures.

  7. Modeling self-excited combustion instabilities using a combination of two- and three-dimensional simulations

    NASA Astrophysics Data System (ADS)

    Harvazinski, Matthew Evan

    Self-excited combustion instabilities have been studied using a combination of two- and three-dimensional computational fluid dynamics (CFD) simulations. This work was undertaken to assess the ability of CFD simulations to generate the high-amplitude resonant combustion dynamics without external forcing or a combustion response function. Specifically, detached eddy simulations (DES), which allow for significantly coarser grid resolutions in wall bounded flows than traditional large eddy simulations (LES), were investigated for their capability of simulating the instability. A single-element laboratory rocket combustor which produces self-excited longitudinal instabilities is used for the configuration. The model rocket combustor uses an injector configuration based on practical oxidizer-rich staged-combustion devices; a sudden expansion combustion section; and uses decomposed hydrogen peroxide as the oxidizer and gaseous methane as the fuel. A better understanding of the physics has been achieved using a series of diagnostics. Standard CFD outputs like instantaneous and time averaged flowfield outputs are combined with other tools, like the Rayleigh index to provide additional insight. The Rayleigh index is used to identify local regions in the combustor which are responsible for driving and damping the instability. By comparing the Rayleigh index to flowfield parameters it is possible to connect damping and driving to specific flowfield conditions. A cost effective procedure to compute multidimensional local Rayleigh index was developed. This work shows that combustion instabilities can be qualitatively simulated using two-dimensional axisymmetric simulations for fuel rich operating conditions. A full three-dimensional simulation produces a higher level of instability which agrees quite well with the experimental results. In addition to matching the level of instability the three-dimensional simulation also predicts the harmonic nature of the instability that is

  8. Building a three-dimensional model of the upper gastrointestinal tract for computer simulations of swallowing.

    PubMed

    Gastelum, Alfonso; Mata, Lucely; Brito-de-la-Fuente, Edmundo; Delmas, Patrice; Vicente, William; Salinas-Vázquez, Martín; Ascanio, Gabriel; Marquez, Jorge

    2016-03-01

    We aimed to provide realistic three-dimensional (3D) models to be used in numerical simulations of peristaltic flow in patients exhibiting difficulty in swallowing, also known as dysphagia. To this end, a 3D model of the upper gastrointestinal tract was built from the color cryosection images of the Visible Human Project dataset. Regional color heterogeneities were corrected by centering local histograms of the image difference between slices. A voxel-based model was generated by stacking contours from the color images. A triangle mesh was built, smoothed and simplified. Visualization tools were developed for browsing the model at different stages and for virtual endoscopy navigation. As result, a computer model of the esophagus and the stomach was obtained, mainly for modeling swallowing disorders. A central-axis curve was also obtained for virtual navigation and to replicate conditions relevant to swallowing disorders modeling. We show renderings of the model and discuss its use for simulating swallowing as a function of bolus rheological properties. The information obtained from simulation studies with our model could be useful for physicians in selecting the correct nutritional emulsions for patients with dysphagia.

  9. Simulation of upper troposphere CO2 from two-dimensional and three-dimensional models

    NASA Astrophysics Data System (ADS)

    Jiang, X.; Shia, R.; Li, Q.; Chahine, M. T.; Olsen, E. T.; Chen, L. L.; Yung, Y. L.

    2006-12-01

    The Caltech/JPL two-dimensional (2-D) chemistry and transport model (CTM) and three-dimensional (3-D) GEOS-CHEM model have been used to simulate the CO2 in the upper troposphere from 2000 to 2004. Model results agree well with the aircraft observations between 9 km and 13 km [Matsueda et al., Tellus 2002] in the tropics. However, in the mid-latitudes there are some discrepancies between the 3-D GEOS-CHEM simulation and 2-D CTM simulation. The 2-D CTM matches the observations better. The comparison of the profiles between the two model simulations reveals that the exchange between the stratosphere and troposphere in the 3-D model may be too strong in the winter and spring. Specific humidity from GEOS-4 model and AIRS is used as a diagnostic of convection in the 3-D GEOS-CHEM model. While the GEOS-4 specific humidity matches that of AIRS fairly well in the tropics, the agreement is poor at mid-latitudes, where the model does not show enough deep convection. Finally, CO2 simulated by 2-D and 3-D models are compared to the CO2 retrieval from Chahine et al. [GRL 2005].

  10. Implicit Three-Dimensional Geo-Modelling Based on HRBF Surface

    NASA Astrophysics Data System (ADS)

    Gou, J.; Zhou, W.; Wu, L.

    2016-10-01

    Three-dimensional (3D) geological models are important representations of the results of regional geological surveys. However, the process of constructing 3D geological models from two-dimensional (2D) geological elements remains difficult and time-consuming. This paper proposes a method of migrating from 2D elements to 3D models. First, the geological interfaces were constructed using the Hermite Radial Basis Function (HRBF) to interpolate the boundaries and attitude data. Then, the subsurface geological bodies were extracted from the spatial map area using the Boolean method between the HRBF surface and the fundamental body. Finally, the top surfaces of the geological bodies were constructed by coupling the geological boundaries to digital elevation models. Based on this workflow, a prototype system was developed, and typical geological structures (e.g., folds, faults, and strata) were simulated. Geological modes were constructed through this workflow based on realistic regional geological survey data. For extended applications in 3D modelling of other kinds of geo-objects, mining ore body models and urban geotechnical engineering stratum models were constructed by this method from drill-hole data. The model construction process was rapid, and the resulting models accorded with the constraints of the original data.

  11. A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells

    PubMed Central

    Drummond, Coyne G.

    2015-01-01

    ABSTRACT Despite serving as the primary entry portal for coxsackievirus B (CVB), little is known about CVB infection of the intestinal epithelium, owing at least in part to the lack of suitable in vivo models and the inability of cultured cells to recapitulate the complexity and structure associated with the gastrointestinal (GI) tract. Here, we report on the development of a three-dimensional (3-D) organotypic cell culture model of Caco-2 cells to model CVB infection of the gastrointestinal epithelium. We show that Caco-2 cells grown in 3-D using the rotating wall vessel (RWV) bioreactor recapitulate many of the properties of the intestinal epithelium, including the formation of well-developed tight junctions, apical-basolateral polarity, brush borders, and multicellular complexity. In addition, transcriptome analyses using transcriptome sequencing (RNA-Seq) revealed the induction of a number of genes associated with intestinal epithelial differentiation and/or intestinal processes in vivo when Caco-2 cells were cultured in 3-D. Applying this model to CVB infection, we found that although the levels of intracellular virus production were similar in two-dimensional (2-D) and 3-D Caco-2 cell cultures, the release of infectious CVB was enhanced in 3-D cultures at early stages of infection. Unlike CVB, the replication of poliovirus (PV) was significantly reduced in 3-D Caco-2 cell cultures. Collectively, our studies show that Caco-2 cells grown in 3-D using the RWV bioreactor provide a cell culture model that structurally and transcriptionally represents key aspects of cells in the human GI tract and can thus be used to expand our understanding of enterovirus-host interactions in intestinal epithelial cells. IMPORTANCE Coxsackievirus B (CVB), a member of the enterovirus family of RNA viruses, is associated with meningitis, pericarditis, diabetes, dilated cardiomyopathy, and myocarditis, among other pathologies. CVB is transmitted via the fecal-oral route and

  12. A Three-Dimensional Cell Culture Model To Study Enterovirus Infection of Polarized Intestinal Epithelial Cells.

    PubMed

    Drummond, Coyne G; Nickerson, Cheryl A; Coyne, Carolyn B

    2016-01-01

    Despite serving as the primary entry portal for coxsackievirus B (CVB), little is known about CVB infection of the intestinal epithelium, owing at least in part to the lack of suitable in vivo models and the inability of cultured cells to recapitulate the complexity and structure associated with the gastrointestinal (GI) tract. Here, we report on the development of a three-dimensional (3-D) organotypic cell culture model of Caco-2 cells to model CVB infection of the gastrointestinal epithelium. We show that Caco-2 cells grown in 3-D using the rotating wall vessel (RWV) bioreactor recapitulate many of the properties of the intestinal epithelium, including the formation of well-developed tight junctions, apical-basolateral polarity, brush borders, and multicellular complexity. In addition, transcriptome analyses using transcriptome sequencing (RNA-Seq) revealed the induction of a number of genes associated with intestinal epithelial differentiation and/or intestinal processes in vivo when Caco-2 cells were cultured in 3-D. Applying this model to CVB infection, we found that although the levels of intracellular virus production were similar in two-dimensional (2-D) and 3-D Caco-2 cell cultures, the release of infectious CVB was enhanced in 3-D cultures at early stages of infection. Unlike CVB, the replication of poliovirus (PV) was significantly reduced in 3-D Caco-2 cell cultures. Collectively, our studies show that Caco-2 cells grown in 3-D using the RWV bioreactor provide a cell culture model that structurally and transcriptionally represents key aspects of cells in the human GI tract and can thus be used to expand our understanding of enterovirus-host interactions in intestinal epithelial cells. IMPORTANCE Coxsackievirus B (CVB), a member of the enterovirus family of RNA viruses, is associated with meningitis, pericarditis, diabetes, dilated cardiomyopathy, and myocarditis, among other pathologies. CVB is transmitted via the fecal-oral route and encounters the

  13. Biomechanical modeling of the three-dimensional aspects of human vocal fold dynamics

    PubMed Central

    Yang, Anxiong; Lohscheller, Jörg; Berry, David A.; Becker, Stefan; Eysholdt, Ulrich; Voigt, Daniel; Döllinger, Michael

    2010-01-01

    Human voice originates from the three-dimensional (3D) oscillations of the vocal folds. In previous studies, biomechanical properties of vocal fold tissues have been predicted by optimizing the parameters of simple two-mass-models to fit its dynamics to the high-speed imaging data from the clinic. However, only lateral and longitudinal displacements of the vocal folds were considered. To extend previous studies, a 3D mass-spring, cover-model is developed, which predicts the 3D vibrations of the entire medial surface of the vocal fold. The model consists of five mass planes arranged in vertical direction. Each plane contains five longitudinal, mass-spring, coupled oscillators. Feasibility of the model is assessed using a large body of dynamical data previously obtained from excised human larynx experiments, in vivo canine larynx experiments, physical models, and numerical models. Typical model output was found to be similar to existing findings. The resulting model enables visualization of the 3D dynamics of the human vocal folds during phonation for both symmetric and asymmetric vibrations. PMID:20136223

  14. Modification of three-dimensional prototype temporal bone model for training in skull-base surgery.

    PubMed

    Mori, Kentaro; Yamamoto, Takuji; Oyama, Kazutaka; Nakao, Yasuaki

    2009-04-01

    Experience with dissection of the temporal bone is essential for training in skull-base surgery, but only a limited number of neurosurgical residents have the opportunity of cadaver dissection. A modification of a commercially available prototype three-dimensional (3D) temporal bone model is proposed to include artificial dura mater, venous sinuses, and cranial nerves for such surgical training. The base 3D temporal bone model incorporates the surface details and the inner ear structures and air cells. Model dural sinuses and dura mater made from silicone, cranial nerves made from rubber fibers, and internal carotid artery made from rubber tubes were added to the model. Posterior petrosectomy (transpetrosal approach) and transcondylar approach were performed on this model using a high-speed drill and ultrasonic bone curette under an operating microscope. The modified 3D temporal bone model provided good experience with the complicated 3D anatomy. The model could be dissected, and the dural sinuses and dura mater preserved by the eggshell peeling technique in almost the same way as real temporal bone. The modified 3D temporal bone model provides a good educational tool for training in skull-base surgery.

  15. Spatial heterogeneity in geothermally-influenced lakes derived from atmospherically corrected Landsat thermal imagery and three-dimensional hydrodynamic modelling

    NASA Astrophysics Data System (ADS)

    Allan, Mathew G.; Hamilton, David P.; Trolle, Dennis; Muraoka, Kohji; McBride, Christopher

    2016-08-01

    Atmospheric correction of Landsat 7 thermal data was carried out for the purpose of retrieval of lake skin water temperature in Rotorua lakes, and Lake Taupo, North Island, New Zealand. The effect of the atmosphere was modelled using four sources of atmospheric profile data as input to the MODerate resolution atmospheric TRANsmission (MODTRAN) radiative transfer model. The retrieved skin water temperatures were validated using a high-frequency temperature sensor deployed from a monitoring buoy at the water surface of Lake Rotorua. The most accurate atmospheric correction method was with Moderate Resolution Imaging Spectroradiometer (MODIS) atmospheric profile data (root-mean-square-error, RMSE, 0.48 K), followed by radiosonde (0.52 K), Atmospheric Infrared Sounder (AIRS) Level 3 (0.54 K), and the NASA atmospheric correction parameter calculator (0.94 K). Retrieved water temperature was used for assessing spatial heterogeneity and accuracy of surface water temperature simulated with a three-dimensional (3-D) hydrodynamic model of Lake Rotoehu, located approximately 20 km east of Lake Rotorua. This comparison indicated that the model was suitable for reproducing the dominant horizontal variations in surface water temperature in the lake. This study demonstrated the potential of accurate satellite-based thermal monitoring to validate temperature outputs from 3-D hydrodynamic model simulations. It also provided atmospheric correction options for local and global applications of Landsat thermal data.

  16. The three-dimensional leading-edge vortex of a 'hovering' model hawkmoth

    PubMed Central

    Berg, C. van den; Ellington, C.P.

    1997-01-01

    Recent flow visualisation experiments with the hawkmoth, Manduca sexta, revealed small but clear leading-edge vortex and a pronounced three-dimensional flow. Details of this flow pattern were studied with a scaled-up, robotic insect ('the flapper') that accurately mimicked the wing movements of a hovering hawkmoth. Smoke released from the leading edge of the flapper wing confirmed the existence of a small, strong and stable leading-edge vortex, increasing in size from wingbase to wingtip. Between 25 and 75 per cent of the wing length, its diameter increased approximately from 10 to 50 per cent of the wing chord. The leading-edge vortex had a strong axial flow veolocity, which stabilized it and reduced its diamater. The vortex separated from the wing at approximately 75 per cent of the wing length and thus fed vorticity into a large, tangled tip vortex. If the circulation of the leading-edge vortex were fully used for lift generation, it could support up to two-thirds of the hawkmoth's weight during the downstroke. The growth of this circulation with time and spanwise position clearly identify dynamic stall as the unsteady aerodynamic mechanism responsible for high lift production by hovering hawkmoths and possibly also by many other insect species.

  17. The Three-Dimensional Leading-Edge Vortex of a "Hovering" Model Hawkmoth

    NASA Astrophysics Data System (ADS)

    van den Berg, Coen; Ellington, Charles P.

    1997-03-01

    Recent flow visualization experiments with the hawkmoth, Manduca sexta, revealed a small but clear leading-edge vortex and a pronounced three-dimensional flow. Details of this flow pattern were studied with a scaled-up, robotic insect ('the flapper') that accurately mimicked the wing movements of a hovering hawkmoth. Smoke released from the leading edge of the flapper wing confirmed the existence of a small, strong and stable leading-edge vortex, increasing in size from wingbase to wingtip. Between 25 and 75% of the wing length, its diameter increased approximately from 10 to 50% of the wing chord. The leading-edge vortex had a strong axial flow velocity, which stabilized it and reduced its diameter. The vortex separated from the wing at approximately 75% of the wing length and thus fed vorticity into a large, tangled tip vortex. If the circulation of the leading-edge vortex were fully used for lift generation, it could support up to two-thirds of the hawkmoth's weight during the downstroke. The growth of this circulation with time and spanwise position clearly identify dynamic stall as the unsteady aerodynamic mechanism responsible for high lift production by hovering hawkmoths and possibly also by many other insect species.

  18. THERMAL AND ELECTROCHEMICAL THREE DIMENSIONAL CFD MODEL OF A PLANAR SOLID OXIDE ELECTROLYSIS CELL

    SciTech Connect

    Grant Hawkes; Jim O'Brien; Carl Stoots; Steve Herring; Mehrdad Shahnam

    2005-07-01

    A three-dimensional computational fluid dynamics (CFD) model has been created to model high-temperature steam electrolysis in a planar solid oxide electrolysis cell (SOEC). The model represents a single cell, as it would exist in an electrolysis stack. Details of the model geometry are specific to a stack that was fabricated by Ceramatec , Inc. and tested at the Idaho National Laboratory. Mass, momentum, energy, and species conservation and transport are provided via the core features of the commercial CFD code FLUENT2. A solid-oxide fuel cell (SOFC) model adds the electrochemical reactions and loss mechanisms and computation of the electric field throughout the cell. The FLUENT SOFC user-defined subroutine was modified for this work to allow for operation in the SOEC mode. Model results provide detailed profiles of temperature, Nernst potential, operating potential, anode-side gas composition, cathode-side gas composition, current density and hydrogen production over a range of stack operating conditions. Mean model results are shown to compare favorably with experimental results obtained from an actual ten-cell stack tested at INL.

  19. Anatomical Reproducibility of a Head Model Molded by a Three-dimensional Printer

    PubMed Central

    KONDO, Kosuke; NEMOTO, Masaaki; MASUDA, Hiroyuki; OKONOGI, Shinichi; NOMOTO, Jun; HARADA, Naoyuki; SUGO, Nobuo; MIYAZAKI, Chikao

    We prepared rapid prototyping models of heads with unruptured cerebral aneurysm based on image data of computed tomography angiography (CTA) using a three-dimensional (3D) printer. The objective of this study was to evaluate the anatomical reproducibility and accuracy of these models by comparison with the CTA images on a monitor. The subjects were 22 patients with unruptured cerebral aneurysm who underwent preoperative CTA. Reproducibility of the microsurgical anatomy of skull bone and arteries, the length and thickness of the main arteries, and the size of cerebral aneurysm were compared between the CTA image and rapid prototyping model. The microsurgical anatomy and arteries were favorably reproduced, apart from a few minute regions, in the rapid prototyping models. No significant difference was noted in the measured lengths of the main arteries between the CTA image and rapid prototyping model, but errors were noted in their thickness (p < 0.001). A significant difference was also noted in the longitudinal diameter of the cerebral aneurysm (p < 0.01). Regarding the CTA image as the gold standard, reproducibility of the microsurgical anatomy of skull bone and main arteries was favorable in the rapid prototyping models prepared using a 3D printer. It was concluded that these models are useful tools for neurosurgical simulation. The thickness of the main arteries and size of cerebral aneurysm should be comprehensively judged including other neuroimaging in consideration of errors. PMID:26119896

  20. Constructing three-dimensional detachable and composable computer models of the head and neck.

    PubMed

    Fan, Min; Dai, Peishan; Zheng, Buhong; Li, Xinchun

    2015-06-01

    The head and neck region has a complex spatial and topological structure, three-dimensional (3D) computer model of the region can be used in anatomical education, radiotherapy planning and surgical training. However, most of the current models only consist of a few parts of the head and neck, and the 3D models are not detachable and composable. In this study, a high-resolution 3D detachable and composable model of the head and neck was constructed based on computed tomography (CT) serial images. First, fine CT serial images of the head and neck were obtained. Then, a color lookup table was created for 58 structures, which was used to create anatomical atlases of the head and neck. Then, surface and volume rendering methods were used to reconstruct 3D models of the head and neck. Smoothing and polygon reduction steps were added to improve 3D rendering effects. 3D computer models of the head and neck, including the sinus, pharynx, vasculature, nervous system, endocrine system and glands, muscles, bones and skin, were reconstructed. The models consisted of 58 anatomical detachable and composable structures and each structure can be displayed individually or together with other structures.

  1. A three-dimensional model of vocal fold abduction/adduction

    NASA Astrophysics Data System (ADS)

    Hunter, Eric J.; Titze, Ingo R.; Alipour, Fariborz

    2004-04-01

    A three-dimensional biomechanical model of tissue deformation was developed to simulate dynamic vocal fold abduction and adduction. The model was made of 1721 nearly incompressible finite elements. The cricoarytenoid joint was modeled as a rocking-sliding motion, similar to two concentric cylinders. The vocal ligament and the thyroarytenoid muscle's fiber characteristics were implemented as a fiber-gel composite made of an isotropic ground substance imbedded with fibers. These fibers had contractile and/or passive nonlinear stress-strain characteristics. The verification of the model was made by comparing the range and speed of motion to published vocal fold kinematic data. The model simulated abduction to a maximum glottal angle of about 31°. Using the posterior-cricoarytenoid muscle, the model produced an angular abduction speed of 405° per second. The system mechanics seemed to favor abduction over adduction in both peak speed and response time, even when all intrinsic muscle properties were kept identical. The model also verified the notion that the vocalis and muscularis portions of the thyroarytenoid muscle play significantly different roles in posturing, with the muscularis portion having the larger effect on arytenoid movement. Other insights into the mechanisms of abduction/adduction were given.

  2. Anatomical Reproducibility of a Head Model Molded by a Three-dimensional Printer.

    PubMed

    Kondo, Kosuke; Nemoto, Masaaki; Masuda, Hiroyuki; Okonogi, Shinichi; Nomoto, Jun; Harada, Naoyuki; Sugo, Nobuo; Miyazaki, Chikao

    2015-01-01

    We prepared rapid prototyping models of heads with unruptured cerebral aneurysm based on image data of computed tomography angiography (CTA) using a three-dimensional (3D) printer. The objective of this study was to evaluate the anatomical reproducibility and accuracy of these models by comparison with the CTA images on a monitor. The subjects were 22 patients with unruptured cerebral aneurysm who underwent preoperative CTA. Reproducibility of the microsurgical anatomy of skull bone and arteries, the length and thickness of the main arteries, and the size of cerebral aneurysm were compared between the CTA image and rapid prototyping model. The microsurgical anatomy and arteries were favorably reproduced, apart from a few minute regions, in the rapid prototyping models. No significant difference was noted in the measured lengths of the main arteries between the CTA image and rapid prototyping model, but errors were noted in their thickness (p < 0.001). A significant difference was also noted in the longitudinal diameter of the cerebral aneurysm (p < 0.01). Regarding the CTA image as the gold standard, reproducibility of the microsurgical anatomy of skull bone and main arteries was favorable in the rapid prototyping models prepared using a 3D printer. It was concluded that these models are useful tools for neurosurgical simulation. The thickness of the main arteries and size of cerebral aneurysm should be comprehensively judged including other neuroimaging in consideration of errors.

  3. Three-dimensional geologic model of the Arbuckle-Simpson aquifer, south-central Oklahoma

    USGS Publications Warehouse

    Faith, Jason R.; Blome, Charles D.; Pantea, Michael P.; Puckette, James O.; Halihan, Todd; Osborn, Noel; Christenson, Scott; Pack, Skip

    2010-01-01

    The Arbuckle-Simpson aquifer of south-central Oklahoma encompasses more than 850 square kilometers and is the principal water resource for south-central Oklahoma. Rock units comprising the aquifer are characterized by limestone, dolomite, and sandstones assigned to two lower Paleozoic units: the Arbuckle and Simpson Groups. Also considered to be part of the aquifer is the underlying Cambrian-age Timbered Hills Group that contains limestone and sandstone. The highly faulted and fractured nature of the Arbuckle-Simpson units and the variable thickness (600 to 2,750 meters) increases the complexity in determining the subsurface geologic framework of this aquifer. A three-dimensional EarthVision (Trademark) geologic framework model was constructed to quantify the geometric relationships of the rock units of the Arbuckle-Simpson aquifer in the Hunton anticline area. This 3-D EarthVision (Trademark) geologic framework model incorporates 54 faults and four modeled units: basement, Arbuckle-Timbered Hills Group, Simpson Group, and post-Simpson. Primary data used to define the model's 54 faults and four modeled surfaces were obtained from geophysical logs, cores, and cuttings from 126 water and petroleum wells. The 3-D framework model both depicts the volumetric extent of the aquifer and provides the stratigraphic layer thickness and elevation data used to construct a MODFLOW version 2000 regional groundwater-flow model.

  4. Thermal Pollution Mathematical Model. Volume 5: User's Manual for Three-Dimensional Rigid-Lid Model. [environment impact of thermal discharges from power plants

    NASA Technical Reports Server (NTRS)

    Lee, S. S.; Sengupta, S.; Nwadike, E. V.; Sinha, S. K.

    1980-01-01

    A user's manual for a three dimensional, rigid lid model used for hydrothermal predictions of closed basins subjected to a heated discharge together with various other inflows and outflows is presented. The model has the capability to predict (1) wind driven circulation; (2) the circulation caused by inflows and outflows to the domain; and (3) the thermal effects in the domain, and to combine the above processes. The calibration procedure consists of comparing ground truth corrected airborne radiometer data with surface isotherms predicted by the model. The model was verified for accuracy at various sites and results are found to be fairly accurate in all verification runs.

  5. Three-dimensional printing of Hela cells for cervical tumor model in vitro.

    PubMed

    Zhao, Yu; Yao, Rui; Ouyang, Liliang; Ding, Hongxu; Zhang, Ting; Zhang, Kaitai; Cheng, Shujun; Sun, Wei

    2014-09-01

    Advances in three-dimensional (3D) printing have enabled the direct assembly of cells and extracellular matrix materials to form in vitro cellular models for 3D biology, the study of disease pathogenesis and new drug discovery. In this study, we report a method of 3D printing for Hela cells and gelatin/alginate/fibrinogen hydrogels to construct in vitro cervical tumor models. Cell proliferation, matrix metalloproteinase (MMP) protein expression and chemoresistance were measured in the printed 3D cervical tumor models and compared with conventional 2D planar culture models. Over 90% cell viability was observed using the defined printing process. Comparisons of 3D and 2D results revealed that Hela cells showed a higher proliferation rate in the printed 3D environment and tended to form cellular spheroids, but formed monolayer cell sheets in 2D culture. Hela cells in 3D printed models also showed higher MMP protein expression and higher chemoresistance than those in 2D culture. These new biological characteristics from the printed 3D tumor models in vitro as well as the novel 3D cell printing technology may help the evolution of 3D cancer study.

  6. Microstructure Analysis and Multi-Unit Cell Model of Three Dimensionally Four-Directional Braided Composites

    NASA Astrophysics Data System (ADS)

    Xu, Kun; Qian, Xiaomei

    2015-02-01

    In this paper, a new multi-unit cell model of three dimensionally braided composites is presented on the basis of the microstructure analysis of 3D braided preforms produced by four-step 1 × 1 method. According to a new unit cell partition scheme, the multi-unit cell model possesses five kinds of unit cells, namely interior, exterior surface, interior surface, exterior corner and interior corner unit cells. Each type of the representative volume cell has unique microstructure and volume fraction in braided composites. On the basis of these five unit cell models, the structural geometry parameters of the preforms are analyzed and the relationship between the structural parameters and the braiding parameters in different regions are derived in detail, such as the braiding angles, fiber volume fraction, yarn packing factor, braiding pitch and so on. Finally, by using the multi-unit cell model, the main structural parameters of braided composites specimens are calculated to validate the effectiveness of the model. The results are in good agreement with the available experimental data. In addition, the effect of braiding angle on the squeezing condition of braiding yarn is analyzed. The variations of the volume proportion of five unit cells to the whole specimen with rows and columns are discussed, respectively. The presented multi-unit cell model can be adopted to design 3D braided composites and predict their mechanical properties.

  7. Effects of fluid structure interaction in a three dimensional model of the spinal subarachnoid space.

    PubMed

    Cheng, Shaokoon; Fletcher, David; Hemley, Sarah; Stoodley, Marcus; Bilston, Lynne

    2014-08-22

    It is unknown whether spinal cord motion has a significant effect on cerebrospinal fluid (CSF) pressure and therefore the importance of including fluid structure interaction (FSI) in computational fluid dynamics models (CFD) of the spinal subarachnoid space (SAS) is unclear. This study aims to determine the effects of FSI on CSF pressure and spinal cord motion in a normal and in a stenosis model of the SAS. A three-dimensional patient specific model of the SAS and spinal cord were constructed from MR anatomical images and CSF flow rate measurements obtained from a healthy human being. The area of SAS at spinal level T4 was constricted by 20% to represent the stenosis model. FSI simulations in both models were performed by running ANSYS CFX and ANSYS Mechanical in tandem. Results from this study show that the effect of FSI on CSF pressure is only about 1% in both the normal and stenosis models and therefore show that FSI has a negligible effect on CSF pressure. PMID:25005435

  8. A reliable method for evaluating upper molar distalization: Superimposition of three-dimensional digital models

    PubMed Central

    Nalcaci, Ruhi; Bicakci, Ali Altug; Ozturk, Firat; Babacan, Hasan

    2015-01-01

    Objective The aim of this study was to evaluate the reliability of measurements obtained after the superimposition of three-dimensional (3D) digital models by comparing them with those obtained from lateral cephalometric radiographs and photocopies of plaster models for the evaluation of upper molar distalization. Methods Data were collected from plaster models and lateral cephalometric radiographs of 20 Class II patients whose maxillary first molars were distalized with an intraoral distalizer. The posterior movements of the maxillary first molars were evaluated using lateral cephalometric radiographs (group CP), photocopies of plaster models (group PH), and digitized 3D models (group TD). Additionally, distalization and expansion of the other teeth and the degrees of molar rotation were measured in group PH and group TD and compared between the two groups. Results No significant difference was observed regarding the amount of molar distalization among the three groups. A comparison of the aforementioned parameters between group PH and group TD did not reveal any significant difference. Conclusions 3D digital models are reliable to assess the results of upper molar distalization and can be considered a valid alternative to conventional measurement methods. PMID:25798414

  9. A new background distribution-based active contour model for three-dimensional lesion segmentation in breast DCE-MRI

    SciTech Connect

    Liu, Hui; Liu, Yiping; Qiu, Tianshuang; Zhao, Zuowei; Zhang, Lina

    2014-08-15

    Purpose: To develop and evaluate a computerized semiautomatic segmentation method for accurate extraction of three-dimensional lesions from dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) of the breast. Methods: The authors propose a new background distribution-based active contour model using level set (BDACMLS) to segment lesions in breast DCE-MRIs. The method starts with manual selection of a region of interest (ROI) that contains the entire lesion in a single slice where the lesion is enhanced. Then the lesion volume from the volume data of interest, which is captured automatically, is separated. The core idea of BDACMLS is a new signed pressure function which is based solely on the intensity distribution combined with pathophysiological basis. To compare the algorithm results, two experienced radiologists delineated all lesions jointly to obtain the ground truth. In addition, results generated by other different methods based on level set (LS) are also compared with the authors’ method. Finally, the performance of the proposed method is evaluated by several region-based metrics such as the overlap ratio. Results: Forty-two studies with 46 lesions that contain 29 benign and 17 malignant lesions are evaluated. The dataset includes various typical pathologies of the breast such as invasive ductal carcinoma, ductal carcinomain situ, scar carcinoma, phyllodes tumor, breast cysts, fibroadenoma, etc. The overlap ratio for BDACMLS with respect to manual segmentation is 79.55% ± 12.60% (mean ± s.d.). Conclusions: A new active contour model method has been developed and shown to successfully segment breast DCE-MRI three-dimensional lesions. The results from this model correspond more closely to manual segmentation, solve the weak-edge-passed problem, and improve the robustness in segmenting different lesions.

  10. Development of a percentile based three-dimensional model of the buttocks in computer system

    NASA Astrophysics Data System (ADS)

    Wang, Lijing; He, Xueli; Li, Hongpeng

    2016-05-01

    There are diverse products related to human buttocks, which need to be designed, manufactured and evaluated with 3D buttock model. The 3D buttock model used in present research field is just simple approximate model similar to human buttocks. The 3D buttock percentile model is highly desired in the ergonomics design and evaluation for these products. So far, there is no research on the percentile sizing system of human 3D buttock model. So the purpose of this paper is to develop a new method for building three-dimensional buttock percentile model in computer system. After scanning the 3D shape of buttocks, the cloud data of 3D points is imported into the reverse engineering software (Geomagic) for the reconstructing of the buttock surface model. Five characteristic dimensions of the buttock are measured through mark-points after models being imported into engineering software CATIA. A series of space points are obtained by the intersecting of the cutting slices and 3D buttock surface model, and then are ordered based on the sequence number of the horizontal and vertical slices. The 1st, 5th, 50th, 95th, 99th percentile values of the five dimensions and the spatial coordinate values of the space points are obtained, and used to reconstruct percentile buttock models. This research proposes a establishing method of percentile sizing system of buttock 3D model based on the percentile values of the ischial tuberosities diameter, the distances from margin to ischial tuberosity and the space coordinates value of coordinate points, for establishing the Nth percentile 3D buttock model and every special buttock types model. The proposed method also serves as a useful guidance for the other 3D percentile models establishment for other part in human body with characteristic points.

  11. Use of a three-dimensional humanized liver model for the study of viral gene vectors.

    PubMed

    Wagner, Anke; Röhrs, Viola; Materne, Eva-Maria; Hiller, Thomas; Kedzierski, Radoslaw; Fechner, Henry; Lauster, Roland; Kurreck, Jens

    2015-10-20

    Reconstituted three-dimensional (3D) liver models obtained by engrafting hepatic cells into an extracellular matrix (ECM) are valuable tools to study tissue regeneration, drug action and toxicology ex vivo. The aim of the present study was to establish a system for the functional investigation of a viral vector in a 3D liver model composed of human HepG2 cells on a rat ECM. An adeno-associated viral (AAV) vector expressing the Emerald green fluorescent protein (EmGFP) and a short hairpin RNA (shRNA) directed against human cyclophilin b (hCycB) was injected into the portal vein of 3D liver models. Application of the vector did not exert toxic effects, as shown by analysis of metabolic parameters. Six days after transduction, fluorescence microscopy analysis of EmGFP production revealed widespread distribution of the AAV vectors. After optimization of the recellularization and transduction conditions, averages of 55 and 90 internalized vector genomes per cell in two replicates of the liver model were achieved, as determined by quantitative PCR analysis. Functionality of the AAV vector was confirmed by efficient shRNA-mediated knockdown of hCycB by 70-90%. Our study provides a proof-of-concept that a recellularized biological ECM provides a valuable model to study viral vectors ex vivo. PMID:26356676

  12. Methods: Using Three-Dimensional Culture (Spheroids) as an In Vitro Model of Tumour Hypoxia.

    PubMed

    Leek, Russell; Grimes, David Robert; Harris, Adrian L; McIntyre, Alan

    2016-01-01

    Regions of hypoxia in tumours can be modelled in vitro in 2D cell cultures with a hypoxic chamber or incubator in which oxygen levels can be regulated. Although this system is useful in many respects, it disregards the additional physiological gradients of the hypoxic microenvironment, which result in reduced nutrients and more acidic pH. Another approach to hypoxia modelling is to use three-dimensional spheroid cultures. In spheroids, the physiological gradients of the hypoxic tumour microenvironment can be inexpensively modelled and explored. In addition, spheroids offer the advantage of more representative modelling of tumour therapy responses compared with 2D culture. Here, we review the use of spheroids in hypoxia tumour biology research and highlight the different methodologies for spheroid formation and how to obtain uniformity. We explore the challenge of spheroid analyses and how to determine the effect on the hypoxic versus normoxic components of spheroids. We discuss the use of high-throughput analyses in hypoxia screening of spheroids. Furthermore, we examine the use of mathematical modelling of spheroids to understand more fully the hypoxic tumour microenvironment. PMID:27325267

  13. Three Dimensional Response Spectrum Soil Structure Modeling Versus Conceptual Understanding To Illustrate Seismic Response Of Structures

    SciTech Connect

    Touqan, Abdul Razzaq

    2008-07-08

    Present methods of analysis and mathematical modeling contain so many assumptions that separate them from reality and thus represent a defect in design which makes it difficult to analyze reasons of failure. Three dimensional (3D) modeling is so superior to 1D or 2D modeling, static analysis deviates from the true nature of earthquake load which is 'a dynamic punch', and conflicting assumptions exist between structural engineers (who assume flexible structures on rigid block foundations) and geotechnical engineers (who assume flexible foundations supporting rigid structures). Thus a 3D dynamic soil-structure interaction is a step that removes many of the assumptions and thus clears reality to a greater extent. However such a model cannot be analytically analyzed. We need to anatomize and analogize it. The paper will represent a conceptual (analogical) 1D model for soil structure interaction and clarifies it by comparing its outcome with 3D dynamic soil-structure finite element analysis of two structures. The aim is to focus on how to calculate the period of the structure and to investigate effect of variation of stiffness on soil-structure interaction.

  14. Computational Study of Effects of Tension Imbalance on Phonation in a Three Dimensional Tubular Larynx Model

    PubMed Central

    Xue, Qian; Zheng, Xudong; Mittal, Rajat; Bielamowicz, Steve

    2014-01-01

    Summary Objective The current study explores the use of a continuum based computational model to investigate the effect of left right tension imbalance on vocal fold vibrations and glottal aerodynamics, as well as its implication on phonation. The study allows us to gain new insights into the underlying physical mechanism of irregularities induced by vocal fold tension imbalance associated with unilateral cricothyroid muscle paralysis. Method A three dimensional simulation of glottal flow and vocal fold dynamics in a tubular laryngeal model with tension imbalance was conducted by using a coupled flow-structure interaction computational model. Tension imbalance was modeled by reducing by 20% the Young’s modulus of one of the vocal folds, while holding vocal fold length constant. Effects of tension imbalance on vibratory characteristic of the vocal folds and on the time-varying properties of glottal airflow as well as the aerodynamic energy transfer are comprehensively analyzed. Results and Conclusions The analysis demonstrates that the continuum based biomechanical model can provide a good description of phonatory dynamics in tension imbalance conditions. It is found that while 20% tension imbalance does not have noticeable effects on the fundamental frequency, it does lead to a larger glottal flow leakage and asymmetric vibrations of the two vocal folds. A detailed analysis of the energy transfer suggests that the majority of the energy is consumed by the lateral motion of the vocal folds and the net energy transferred to the softer fold is less than the one transferred to the normal fold. PMID:24725589

  15. Development of three-dimensional magnetohydrodynamic model for solar corona and solar wind simulation

    NASA Astrophysics Data System (ADS)

    Yuan, Xingqiu; Trichtchenko, Larisa; Boteler, David

    Propagation of coronal mass ejections from solar surface to the Earth magnetosphere is strongly influenced by the conditions in solar corona and ambient solar wind. Thus, reliable simulation of the background solar wind is the primary task toward the development of numerical model for the transient events. In this paper we introduce a new numerical model which has been specifically designed for numerical study of the solar corona and ambient solar wind. This model is based on our recently developed three-dimensional Spherical Coordinate Adaptive Magneto-Hydro-Dynamic (MHD) code (SCA-MHD-3D) [Yuan et al., 2009]. Modifications has been done to include the observed magnetic field at the photosphere as inner boundary conditions. The energy source term together with reduced plasma gamma are used in the nonlinear MHD equations in order to simulate the solar wind acceleration from subsonic speed at solar surface to supersonic speed at the inter-heliosphere region, and the absorbing boundary conditions are used at the solar surface. This model has been applied to simulate the background solar wind condition for several different solar rotations, and comparison between the observation and model output have shown that it reproduces many features of solar wind, including open and closed magnetic fields, fast and slow solar wind speed, sector boundaries, etc.

  16. Effective viscosity of bacterial suspensions: a three-dimensional PDE model with stochastic torque.

    SciTech Connect

    Haines, B. M.; Aranson, I. S.; Berlyand, L.; Karpeev, D. A.

    2012-01-01

    We present a PDE model for dilute suspensions of swimming bacteria in a three-dimensional Stokesian fluid. This model is used to calculate the statistically-stationary bulk deviatoric stress and effective viscosity of the suspension from the microscopic details of the interaction of an elongated body with the background flow. A bacterium is modeled as an impenetrable prolate spheroid with self-propulsion provided by a point force, which appears in the model as an inhomogeneous delta function in the PDE. The bacterium is also subject to a stochastic torque in order to model tumbling (random reorientation). Due to a bacterium's asymmetric shape, interactions with prescribed generic planar background flows, such as a pure straining or planar shear flow, cause the bacterium to preferentially align in certain directions. Due to the stochastic torque, the steady-state distribution of orientations is unique for a given background flow. Under this distribution of orientations, self-propulsion produces a reduction in the effective viscosity. For sufficiently weak background flows, the effect of self-propulsion on the effective viscosity dominates all other contributions, leading to an effective viscosity of the suspension that is lower than the viscosity of the ambient fluid. This is in qualitative agreement with recent experiments on suspensions of Bacillus subtilis.

  17. Three-Dimensional Modeling of Flow and Thermochemical Behavior in a Blast Furnace

    NASA Astrophysics Data System (ADS)

    Shen, Yansong; Guo, Baoyu; Chew, Sheng; Austin, Peter; Yu, Aibing

    2015-02-01

    An ironmaking blast furnace (BF) is a complex high-temperature moving bed reactor involving counter-, co- and cross-current flows of gas, liquid and solid, coupled with heat and mass exchange and chemical reactions. Two-dimensional (2D) models were widely used for understanding its internal state in the past. In this paper, a three-dimensional (3D) CFX-based mathematical model is developed for describing the internal state of a BF in terms of multiphase flow and the related thermochemical behavior, as well as process indicators. This model considers the intense interactions between gas, solid and liquid phases, and also their competition for the space. The model is applied to a BF covering from the burden surface at the top to the liquid surface in the hearth, where the raceway cavity is considered explicitly. The results show that the key in-furnace phenomena such as flow/temperature patterns and component distributions of solid, gas and liquid phases can be described and characterized in different regions inside the BF, including the gas and liquids flow circumferentially over the 3D raceway surface. The in-furnace distributions of key performance indicators such as reduction degree and gas utilization can also be predicted. This model offers a cost-effective tool to understand and control the complex BF flow and performance.

  18. Constitutive modelling of arteries considering fibre recruitment and three-dimensional fibre distribution.

    PubMed

    Weisbecker, Hannah; Unterberger, Michael J; Holzapfel, Gerhard A

    2015-04-01

    Structurally motivated material models may provide increased insights into the underlying mechanics and physics of arteries under physiological loading conditions. We propose a multiscale model for arterial tissue capturing three different scales (i) a single collagen fibre; (ii) bundle of collagen fibres; and (iii) collagen network within the tissue. The waviness of collagen fibres is introduced by a probability density function for the recruitment stretch at which the fibre starts to bear load. The three-dimensional distribution of the collagen fibres is described by an orientation distribution function using the bivariate von Mises distribution, and fitted to experimental data. The strain energy for the tissue is decomposed additively into a part related to the matrix material and a part for the collagen fibres. Volume fractions account for the matrix/fibre constituents. The proposed model only uses two parameters namely a shear modulus of the matrix material and a (stiffness) parameter related to a single collagen fibre. A fit of the multiscale model to representative experimental data obtained from the individual layers of a human thoracic aorta shows that the proposed model is able to adequately capture the nonlinear and anisotropic behaviour of the aortic layers.

  19. Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies

    NASA Astrophysics Data System (ADS)

    Wang, Xiping; Guo, Yan; Li, Baoguo; Wang, Xiyong; Ma, Yuntao

    2006-07-01

    Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize ( Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R 2 equaling 0.78 ( n=120).

  20. Three-Dimensional Electromagnetic Plasma Modeling of Inductively Coupled Plasma Source and Antenna

    NASA Astrophysics Data System (ADS)

    Rauf, Shahid; Agarwal, Ankur; Kenney, Jason; Wu, Ming-Feng; Collins, Ken

    2012-10-01

    Inductively coupled plasmas (ICP) are widely used for etching and deposition in the semiconductor industry. As device dimensions shrink with concomitant decreased tolerance for variability, it is critical to improve plasma and process uniformity in all plasma processes. In ICP systems, one of the major sources of non-uniformity is the radio-frequency (RF) antenna used to generate the electromagnetic wave. Discontinuities at current feed and grounding locations as well as electromagnetic field variations along the antenna coils can perturb the azimuthal electric field, resulting in a non-uniform plasma. For plasma modeling of ICP systems, a related problem is how capacitive coupling from the antenna is accounted for. ICP models have generally considered field variation along the antenna and capacitive coupling using simplified circuit models for the antenna structures. Modern ICP antennas are however quite complicated, making circuit approximations of the antenna too crude for system design. A three-dimensional parallel plasma model is described in this paper, where the full set of Maxwell equations are solved in conjunction with plasma transport equations for the plasma and the antenna. Several examples from the use of this model in ICP system design are presented.

  1. Use of a three-dimensional humanized liver model for the study of viral gene vectors.

    PubMed

    Wagner, Anke; Röhrs, Viola; Materne, Eva-Maria; Hiller, Thomas; Kedzierski, Radoslaw; Fechner, Henry; Lauster, Roland; Kurreck, Jens

    2015-10-20

    Reconstituted three-dimensional (3D) liver models obtained by engrafting hepatic cells into an extracellular matrix (ECM) are valuable tools to study tissue regeneration, drug action and toxicology ex vivo. The aim of the present study was to establish a system for the functional investigation of a viral vector in a 3D liver model composed of human HepG2 cells on a rat ECM. An adeno-associated viral (AAV) vector expressing the Emerald green fluorescent protein (EmGFP) and a short hairpin RNA (shRNA) directed against human cyclophilin b (hCycB) was injected into the portal vein of 3D liver models. Application of the vector did not exert toxic effects, as shown by analysis of metabolic parameters. Six days after transduction, fluorescence microscopy analysis of EmGFP production revealed widespread distribution of the AAV vectors. After optimization of the recellularization and transduction conditions, averages of 55 and 90 internalized vector genomes per cell in two replicates of the liver model were achieved, as determined by quantitative PCR analysis. Functionality of the AAV vector was confirmed by efficient shRNA-mediated knockdown of hCycB by 70-90%. Our study provides a proof-of-concept that a recellularized biological ECM provides a valuable model to study viral vectors ex vivo.

  2. Three-dimensional unstructured-mesh eutrophication model and its application to the Xiangxi River, China.

    PubMed

    Li, Jian; Li, Danxun; Wang, Xingkui

    2012-01-01

    The Xiangxi River is one of the main tributaries in the Three Gorges reservoir, with the shortest distance to the Three Gorges Project Dam. Severe and frequent algal bloom events have occurred frequently in the Xiangxi River in recent years. Therefore, the current study develops a three-dimensional unstructured-mesh model to investigate the dynamic process of algal bloom. The developed model comprises three modules, namely, hydrodynamics, nutrient cycles, and phytoplankton ecological dynamics. A number of factors, including hydrodynamic condition, nutrient concentration, temperature, and light illumination, that would affect the evolution of phytoplankton were considered. Moreover, the wave equation was used to solve the free surface fluctuations and vertical Z-coordinates with adjustable layered thicknesses. These values, in turn, are suitable for solving the algal bloom problems that occurred in the river style reservoir that has a complex boundary and dramatically changing hydrodynamic conditions. The comparisons between the modeling results and field data of years 2007 and 2008 indicate that the developed model is capable of simulating the algal bloom process in the Xiangxi River with reasonable accuracy. However, hydrodynamic force and external pollution loads affect the concentrations of nutrients, which, along with the underwater light intensity, could consequently affect phytoplankton evolution. Thus, flow velocity cannot be ignored in the analysis of river algal bloom. Based on the modeling results, building an impounding reservoir and increasing the releasing discharge at appropriate times are effective ways for controlling algal bloom.

  3. Development and validation of a three-dimensional finite element model of the face.

    PubMed

    Barbarino, G G; Jabareen, M; Trzewik, J; Nkengne, A; Stamatas, G; Mazza, E

    2009-04-01

    A detailed three-dimensional finite element model of the face is presented in this paper. Bones, muscles, skin, fat, and superficial muscoloaponeurotic system were reconstructed from magnetic resonance images and modeled according to anatomical, plastic, and reconstructive surgery literature. The finite element mesh, composed of hexahedron elements, was generated through a semi-automatic procedure with an effective compromise between the detailed representation of anatomical parts and the limitation of the computational time. Nonlinear constitutive equations are implemented in the finite element model. The corresponding model parameters were selected according to previous work with mechanical measurements on soft facial tissue, or based on reasonable assumptions. Model assumptions concerning tissue geometry, interactions, mechanical properties, and the boundary conditions were validated through comparison with experiments. The calculated response of facial tissues to gravity loads, to the application of a pressure inside the oral cavity and to the application of an imposed displacement was shown to be in good agreement with the data from corresponding magnetic resonance images and holographic measurements. As a first application, gravimetric soft tissue descent was calculated from the long time action of gravity on the face in the erect position, with tissue aging leading to a loss of stiffness. Aging predictions are compared with the observations from an "aging database" with frontal photos of volunteers at different age ranges (i.e., 20-40 years and 50-70 years). PMID:19275435

  4. Three-Dimensional Computational Fluid Dynamics Modeling of Solid Oxide Electrolysis Cells and Stacks

    SciTech Connect

    Grant Hawkes; James O'Brien; Carl Stoots; Stephen Herring

    2008-07-01

    A three-dimensional computational fluid dynamics (CFD) electrochemical model has been created for detailed analysis of a high-temperature electrolysis stack (solid oxide fuel cells operated as electrolyzers). Inlet and outlet plenum flow distributions are discussed. Maldistribution of plena flow show deviations in per-cell operating conditions due to non-uniformity of species concentrations. Models have also been created to simulate experimental conditions and for code validation. Comparisons between model predictions and experimental results are discussed. Mass, momentum, energy, and species conservation and transport are provided via the core features of the commercial CFD code FLUENT. A solid-oxide fuel cell (SOFC) model adds the electrochemical reactions and loss mechanisms and computation of the electric field throughout the cell. The FLUENT SOFC user-defined subroutine was modified for this work to allow for operation in the electrolysis mode. Model results provide detailed profiles of temperature, Nernst potential, operating potential, activation over-potential, anode-side gas composition, cathode-side gas composition, current density and hydrogen production over a range of stack operating conditions. Variations in flow distribution, and species concentration are discussed. End effects of flow and per-cell voltage are also considered. Predicted mean outlet hydrogen and steam concentrations vary linearly with current density, as expected. Contour plots of local electrolyte temperature, current density, and Nernst potential indicate the effects of heat transfer, reaction cooling/heating, and change in local gas composition.

  5. Development of a three-dimensional model of the human respiratory system for dosimetric use

    PubMed Central

    2013-01-01

    Background Determining the fate of inhaled contaminants in the human respiratory system has challenged scientists for years. Human and animal studies have provided some data, but there is a paucity of data for toxic contaminants and sensitive populations (such as children, elderly, diseased). Methods Three-dimensional modeling programs and publicly available human physiology data have been used to develop a comprehensive model of the human respiratory system. Results The in silico human respiratory system model, which includes the extrathoracic region (nasal, oral, pharyngeal, and laryngeal passages), the upper airways (trachea and main bronchi), the tracheobronchial tree, and branching networks through alveolar region, allows for virtually any variation of airway geometries and disease states. The model allows for parameterization of variables that define the subject’s airways by integrating morphological changes created by disease, age, etc. with a dynamic morphology. Conclusions The model can be used for studies of sensitive populations and the homeland security community, in cases where inhalation studies on humans cannot be conducted with toxic contaminants of interest. PMID:23634755

  6. Computational synthesis of ultrasound breast images from a three-dimensional anatomical model

    NASA Astrophysics Data System (ADS)

    Shen, Yi-Ting; Lacefield, James C.

    2005-04-01

    A three-dimensional breast anatomy model has been implemented using spline surfaces and fractal structures to represent the architecture of the lactiferous ducts, mammary fat lobules, skin, and supporting connective tissues. The model randomly varies user-specified structural parameters to provide an unlimited number of realizations of the gross anatomy. Cross-sectional views extracted by slicing through a realization of the model are input to a two-dimensional k-space (i.e., spatial frequency domain) ultrasound propagation simulator. The k-space simulator iterates pressure and particle velocity fields in 30-ns steps to compute scattering from the structures defined by the anatomical model and small random variations in compressibility that are added to generate speckle. A synthetic aperture method is employed to simulate B-mode imaging with a 5 MHz, 192-element linear array operated using multiple transmit focal zones and dynamic receive focusing. Simulated images of random-scattering phantoms possess approximately Rayleigh speckle statistics. The anatomical model is expected to yield images with speckle statistics comparable to clinical breast images. The long-term objectives of these simulations are to investigate sources of focus aberration in ultrasound breast imaging and the impact of aberration on cancer detection. [Work supported by an NSERC Discovery Grant.

  7. Three-dimensional unstructured-mesh eutrophication model and its application to the Xiangxi River, China.

    PubMed

    Li, Jian; Li, Danxun; Wang, Xingkui

    2012-01-01

    The Xiangxi River is one of the main tributaries in the Three Gorges reservoir, with the shortest distance to the Three Gorges Project Dam. Severe and frequent algal bloom events have occurred frequently in the Xiangxi River in recent years. Therefore, the current study develops a three-dimensional unstructured-mesh model to investigate the dynamic process of algal bloom. The developed model comprises three modules, namely, hydrodynamics, nutrient cycles, and phytoplankton ecological dynamics. A number of factors, including hydrodynamic condition, nutrient concentration, temperature, and light illumination, that would affect the evolution of phytoplankton were considered. Moreover, the wave equation was used to solve the free surface fluctuations and vertical Z-coordinates with adjustable layered thicknesses. These values, in turn, are suitable for solving the algal bloom problems that occurred in the river style reservoir that has a complex boundary and dramatically changing hydrodynamic conditions. The comparisons between the modeling results and field data of years 2007 and 2008 indicate that the developed model is capable of simulating the algal bloom process in the Xiangxi River with reasonable accuracy. However, hydrodynamic force and external pollution loads affect the concentrations of nutrients, which, along with the underwater light intensity, could consequently affect phytoplankton evolution. Thus, flow velocity cannot be ignored in the analysis of river algal bloom. Based on the modeling results, building an impounding reservoir and increasing the releasing discharge at appropriate times are effective ways for controlling algal bloom. PMID:23520863

  8. A California statewide three-dimensional seismic velocity model from both absolute and differential times

    USGS Publications Warehouse

    Lin, G.; Thurber, C.H.; Zhang, H.; Hauksson, E.; Shearer, P.M.; Waldhauser, F.; Brocher, T.M.; Hardebeck, J.

    2010-01-01

    We obtain a seismic velocity model of the California crust and uppermost mantle using a regional-scale double-difference tomography algorithm. We begin by using absolute arrival-time picks to solve for a coarse three-dimensional (3D) P velocity (VP) model with a uniform 30 km horizontal node spacing, which we then use as the starting model for a finer-scale inversion using double-difference tomography applied to absolute and differential pick times. For computational reasons, we split the state into 5 subregions with a grid spacing of 10 to 20 km and assemble our final statewide VP model by stitching together these local models. We also solve for a statewide S-wave model using S picks from both the Southern California Seismic Network and USArray, assuming a starting model based on the VP results and a VP=VS ratio of 1.732. Our new model has improved areal coverage compared with previous models, extending 570 km in the SW-NE directionand 1320 km in the NW-SE direction. It also extends to greater depth due to the inclusion of substantial data at large epicentral distances. Our VP model generally agrees with previous separate regional models for northern and southern California, but we also observe some new features, such as high-velocity anomalies at shallow depths in the Klamath Mountains and Mount Shasta area, somewhat slow velocities in the northern Coast Ranges, and slow anomalies beneath the Sierra Nevada at midcrustal and greater depths. This model can be applied to a variety of regional-scale studies in California, such as developing a unified statewide earthquake location catalog and performing regional waveform modeling.

  9. Analytic Study of Three-Dimensional Rupture Propagation in Strike-Slip Faulting with Analogue Models

    NASA Astrophysics Data System (ADS)

    Chan, Pei-Chen; Chu, Sheng-Shin; Lin, Ming-Lang

    2014-05-01

    Strike-slip faults are high angle (or nearly vertical) fractures where the blocks have moved along strike way (nearly horizontal). Overburden soil profiles across main faults of Strike-slip faults have revealed the palm and tulip structure characteristics. McCalpin (2005) has trace rupture propagation on overburden soil surface. In this study, we used different offset of slip sandbox model profiles to study the evolution of three-dimensional rupture propagation by strike -slip faulting. In strike-slip faults model, type of rupture propagation and width of shear zone (W) are primary affecting by depth of overburden layer (H), distances of fault slip (Sy). There are few research to trace of three-dimensional rupture behavior and propagation. Therefore, in this simplified sandbox model, investigate rupture propagation and shear zone with profiles across main faults when formation are affecting by depth of overburden layer and distances of fault slip. The investigators at the model included width of shear zone, length of rupture (L), angle of rupture (θ) and space of rupture. The surface results was follow the literature that the evolution sequence of failure envelope was R-faults, P-faults and Y-faults which are parallel to the basement fault. Comparison surface and profiles structure which were curved faces and cross each other to define 3-D rupture and width of shear zone. We found that an increase in fault slip could result in a greater width of shear zone, and proposed a W/H versus Sy/H relationship. Deformation of shear zone showed a similar trend as in the literature that the increase of fault slip resulted in the increase of W, however, the increasing trend became opposite after a peak (when Sy/H was 1) value of W was reached (small than 1.5). The results showed that the W width is limited at a constant value in 3-D models by strike-slip faulting. In conclusion, this study helps evaluate the extensions of the shear zone influenced regions for strike

  10. Percutaneous Transcatheter Mitral Valve Replacement: Patient-specific Three-dimensional Computer-based Heart Model and Prototyping.

    PubMed

    Vaquerizo, Beatriz; Theriault-Lauzier, Pascal; Piazza, Nicolo

    2015-12-01

    Mitral regurgitation is the most prevalent valvular heart disease worldwide. Despite the widespread availability of curative surgical intervention, a considerable proportion of patients with severe mitral regurgitation are not referred for treatment, largely due to the presence of left ventricular dysfunction, advanced age, and comorbid illnesses. Transcatheter mitral valve replacement is a promising therapeutic alternative to traditional surgical valve replacement. The complex anatomical and pathophysiological nature of the mitral valvular complex, however, presents significant challenges to the successful design and implementation of novel transcatheter mitral replacement devices. Patient-specific 3-dimensional computer-based models enable accurate assessment of the mitral valve anatomy and preprocedural simulations for transcatheter therapies. Such information may help refine the design features of novel transcatheter mitral devices and enhance procedural planning. Herein, we describe a novel medical image-based processing tool that facilitates accurate, noninvasive assessment of the mitral valvular complex, by creating precise three-dimensional heart models. The 3-dimensional computer reconstructions are then converted to a physical model using 3-dimensional printing technology, thereby enabling patient-specific assessment of the interaction between device and patient. It may provide new opportunities for a better understanding of the mitral anatomy-pathophysiology-device interaction, which is of critical importance for the advancement of transcatheter mitral valve replacement.

  11. Evaluation of three-dimensional anisotropic head model for mapping realistic electromagnetic fields of brain tissues

    NASA Astrophysics Data System (ADS)

    Jeong, Woo Chul; Wi, Hun; Sajib, Saurav Z. K.; Oh, Tong In; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2015-08-01

    Electromagnetic fields provide fundamental data for the imaging of electrical tissue properties, such as conductivity and permittivity, in recent magnetic resonance (MR)-based tissue property mapping. The induced voltage, current density, and magnetic flux density caused by externally injected current are critical factors for determining the image quality of electrical tissue conductivity. As a useful tool to identify bio-electromagnetic phenomena, precise approaches are required to understand the exact responses inside the human body subject to an injected currents. In this study, we provide the numerical simulation results of electromagnetic field mapping of brain tissues using a MR-based conductivity imaging method. First, we implemented a realistic three-dimensional human anisotropic head model using high-resolution anatomical and diffusion tensor MR images. The voltage, current density, and magnetic flux density of brain tissues were imaged by injecting 1 mA of current through pairs of electrodes on the surface of our head model. The current density map of anisotropic brain tissues was calculated from the measured magnetic flux density based on the linear relationship between the water diffusion tensor and the electrical conductivity tensor. Comparing the current density to the previous isotropic model, the anisotropic model clearly showed the differences between the brain tissues. This originates from the enhanced signals by the inherent conductivity contrast as well as the actual tissue condition resulting from the injected currents.

  12. Modelling of multiscale nonlinear interaction of elastic waves with three-dimensional cracks.

    PubMed

    Ciampa, Francesco; Barbieri, Ettore; Meo, Michele

    2014-06-01

    This paper presents a nonlinear elastic material model able to simulate the nonlinear effects generated by the interaction of acoustic/ultrasonic waves with damage precursors and micro-cracks in a variety of materials. Such a constitutive model is implemented in an in-house finite element code and exhibits a multiscale nature where the macroscopic behavior of damaged structures can be represented through a contribution of a number of mesoscopic elements, which are composed by a statistical collection of microscopic units. By means of the semi-analytical Landau formulation and Preisach-Mayergoyz space representation, this multiscale model allows the description of the structural response under continuous harmonic excitation of micro-damaged materials showing both anharmonic and dissipative hysteretic effects. In this manner, nonlinear effects observed experimentally, such as the generation of both even and odd harmonics, can be reproduced. In addition, by using Kelvin eigentensors and eigenelastic constants, the wave propagation problem in both isotropic and orthotropic solids was extended to the three-dimensional Cartesian space. The developed model has been verified for a number of different geometrical and material configurations. Particularly, the influence of a small region with classical and non-classical elasticity and the variations of the input amplitudes on the harmonics generation were analyzed.

  13. Three-dimensional virtual surgery models for percutaneous coronary intervention (PCI) optimization strategies.

    PubMed

    Wang, Hujun; Liu, Jinghua; Zheng, Xu; Rong, Xiaohui; Zheng, Xuwei; Peng, Hongyu; Silber-Li, Zhanghua; Li, Mujun; Liu, Liyu

    2015-06-04

    Percutaneous coronary intervention (PCI), especially coronary stent implantation, has been shown to be an effective treatment for coronary artery disease. However, in-stent restenosis is one of the longstanding unsolvable problems following PCI. Although stents implanted inside narrowed vessels recover normal flux of blood flows, they instantaneously change the wall shear stress (WSS) distribution on the vessel surface. Improper stent implantation positions bring high possibilities of restenosis as it enlarges the low WSS regions and subsequently stimulates more epithelial cell outgrowth on vessel walls. To optimize the stent position for lowering the risk of restenosis, we successfully established a digital three-dimensional (3-D) model based on a real clinical coronary artery and analysed the optimal stenting strategies by computational simulation. Via microfabrication and 3-D printing technology, the digital model was also converted into in vitro microfluidic models with 3-D micro channels. Simultaneously, physicians placed real stents inside them; i.e., they performed "virtual surgeries". The hydrodynamic experimental results showed that the microfluidic models highly inosculated the simulations. Therefore, our study not only demonstrated that the half-cross stenting strategy could maximally reduce restenosis risks but also indicated that 3-D printing combined with clinical image reconstruction is a promising method for future angiocardiopathy research.

  14. Three-dimensional virtual surgery models for percutaneous coronary intervention (PCI) optimization strategies

    NASA Astrophysics Data System (ADS)

    Wang, Hujun; Liu, Jinghua; Zheng, Xu; Rong, Xiaohui; Zheng, Xuwei; Peng, Hongyu; Silber-Li, Zhanghua; Li, Mujun; Liu, Liyu

    2015-06-01

    Percutaneous coronary intervention (PCI), especially coronary stent implantation, has been shown to be an effective treatment for coronary artery disease. However, in-stent restenosis is one of the longstanding unsolvable problems following PCI. Although stents implanted inside narrowed vessels recover normal flux of blood flows, they instantaneously change the wall shear stress (WSS) distribution on the vessel surface. Improper stent implantation positions bring high possibilities of restenosis as it enlarges the low WSS regions and subsequently stimulates more epithelial cell outgrowth on vessel walls. To optimize the stent position for lowering the risk of restenosis, we successfully established a digital three-dimensional (3-D) model based on a real clinical coronary artery and analysed the optimal stenting strategies by computational simulation. Via microfabrication and 3-D printing technology, the digital model was also converted into in vitro microfluidic models with 3-D micro channels. Simultaneously, physicians placed real stents inside them; i.e., they performed “virtual surgeries”. The hydrodynamic experimental results showed that the microfluidic models highly inosculated the simulations. Therefore, our study not only demonstrated that the half-cross stenting strategy could maximally reduce restenosis risks but also indicated that 3-D printing combined with clinical image reconstruction is a promising method for future angiocardiopathy research.

  15. Three-dimensional geologic modeling and visualization of the Virttaankangas aquifer, southwestern Finland

    USGS Publications Warehouse

    Artimo, A.; Makinen, J.; Berg, R.C.; Abert, C.C.; Salonen, V.-P.

    2003-01-01

    A need exists for a reliable and long-term water supply for the 285,000 inhabitants of the Turku area in southwestern Finland. In response to this need, there are plans to replace the present water supply from the surface sources with artificially infiltrated groundwater from a Quaternary esker aquifer called the Virttaankangas aquifer. New sedimentological studies of the Virttaankangas area have revealed the complexities of the esker system and its surrounding glacial, glaciofluvial, and glaciolacustrine geology. This led to the characterization of the hydrogeological units of the aquifer, the result of which has been a three-dimensional (3-D) truly integrated solids model that represents the geometry, interrelationships, and hydrostratigraphy of the study area. The 3-D model was made with Earth Vision geologic modeling software. The 3-D geological model of the Virttaankangas aquifer can be used for planning the infiltration of river water into the aquifer and to understand the geologic and geographic boundaries of the hydrogeologic units hosting the groundwater reserve and the geologic relationships between the units. Another major outcome of this study is a powerful visualization tool that will be provided to municipal and government authorities who must understand the geologic complexities involved with water-resource planning prior to their decision making.

  16. Wintertime nitric acid chemistry - Implications from three-dimensional model calculations

    NASA Technical Reports Server (NTRS)

    Rood, Richard B.; Kaye, Jack A.; Douglass, Anne R.; Allen, Dale J.; Steenford, Stephen

    1990-01-01

    A three-dimensional simulation of the evolution of HNO3 has been run for the winter of 1979. Winds and temperatures are taken from a stratospheric data assimilation analysis, and the chemistry is based on Limb Infrared Monitor of the Stratosphere (LIMS) observations. The model is compared to LIMS observations to investigate the problem of 'missing' nitric acid chemistry in the winter hemisphere. Both the model and observations support the contention that a nitric acid source is needed outside of the polar vortex and north of the subtropics. Observations suggest that HNO3 is not dynamically controlled in middle latitudes. The model shows that given the time scales of conventional chemistry, dynamical control is expected. Therefore, an error exists in the conventional chemistry or additional processes are needed to bring the model and data into agreement. Since the polar vortex is dynamically isolated from the middle latitudes, and since the highest HNO3 values are observed in October and November, a source associated solely with polar stratospheric clouds cannot explain the deficiencies in the chemistry. The role of heterogeneous processes on background aerosols is reviewed in light of these results.

  17. Three-dimensional model of a selective theophylline-binding RNA molecule

    SciTech Connect

    Tung, Chang-Shung; Oprea, T.I.; Hummer, G.; Garcia, A.E.

    1995-07-01

    We propose a three-dimensional (3D) model for an RNA molecule that selectively binds theophylline but not caffeine. This RNA, which was found using SELEX [Jenison, R.D., et al., Science (1994) 263:1425] is 10,000 times more specific for theophylline (Kd=320 nM) than for caffeine (Kd=3.5 mM), although the two ligands are identical except for a methyl group substituted at N7 (present only in caffeine). The binding affinity for ten xanthine-based ligands was used to derive a Comparative Molecular Field Analysis (CoMFA) model (R{sup 2} = 0.93 for 3 components, with cross-validated R{sup 2} of 0.73), using the SYBYL and GOLPE programs. A pharmacophoric map was generated to locate steric and electrostatic interactions between theophylline and the RNA binding site. This information was used to identify putative functional groups of the binding pocket and to generate distance constraints. Based on a model for the secondary structure (Jenison et al., idem), the 3D structure of this RNA was then generated using the following method: each helical region of the RNA molecule was treated as a rigid body; single-stranded loops with specific end-to-end distances were generated. The structures of RNA-xanthine complexes were studied using a modified Monte Carlo algorithm. The detailed structure of an RNA-ligand complex model, as well as possible explanations for the theophylline selectivity will be discussed.

  18. Three-dimensional model for meta-II rhodopsin, an activated G-protein-coupled receptor.

    PubMed

    Nikiforovich, Gregory V; Marshall, Garland R

    2003-08-01

    A novel approach that iteratively combined the results of energy calculations and experimental data was used to generate a three-dimensional (3D) model of the photoactivated state (R*) of bovine rhodopsin (Rh). The approach started with simplified energy calculations in an effort to find a set of sterically and energetically reasonable options for transmembrane (TM) helix arrangements with all-trans-retinal. Various 3D models of TM helix packing found by computations were then compared to limited site-directed spin-label experimental data regarding the transition of the TM helices of Rh in the inactive state (R) to those in the R* state to identify the most plausible model of the TM helical bundle. At the next step, all non-TM structural elements, such as the non-TM helix 8, the N- and C-terminal fragments, and the loops connecting TM helices, were reconstructed, and after the entire R* structure had been relaxed, all other currently available additional experimental data, both mutational and spectroscopic, on the structure of the meta-II state of rhodopsin were used to validate the resulting 3D model.

  19. Leading-order cross term correction of three-dimensional parabolic equation models.

    PubMed

    Sturm, Frédéric

    2016-01-01

    The issue of handling a leading-order cross-multiplied term in three-dimensional (3D) parabolic equation (PE) based models is addressed. In particular, numerical results obtained incorporating a leading-order cross-term correction in an existing 3D PE model, written in cylindrical coordinates, based on higher-order Padé approximations in both depth and azimuth, and a splitting operator technique are reported. Note that the numerical algorithm proposed in this paper could be used in the future to update any 3D PE codes that neglect cross terms and use a splitting numerical technique. The 3D penetrable wedge benchmark problem is chosen to illustrate the accuracy of the now-fully wide-angle enhanced 3D PE model. The comparisons with a 3D reference solution based on the image source clearly show that handling the leading-order cross term in the 3D PE computation is sufficient to remove the phase errors inherent to any 3D PE models that neglect cross terms in their formulations.

  20. Three-dimensional virtual surgery models for percutaneous coronary intervention (PCI) optimization strategies.

    PubMed

    Wang, Hujun; Liu, Jinghua; Zheng, Xu; Rong, Xiaohui; Zheng, Xuwei; Peng, Hongyu; Silber-Li, Zhanghua; Li, Mujun; Liu, Liyu

    2015-01-01

    Percutaneous coronary intervention (PCI), especially coronary stent implantation, has been shown to be an effective treatment for coronary artery disease. However, in-stent restenosis is one of the longstanding unsolvable problems following PCI. Although stents implanted inside narrowed vessels recover normal flux of blood flows, they instantaneously change the wall shear stress (WSS) distribution on the vessel surface. Improper stent implantation positions bring high possibilities of restenosis as it enlarges the low WSS regions and subsequently stimulates more epithelial cell outgrowth on vessel walls. To optimize the stent position for lowering the risk of restenosis, we successfully established a digital three-dimensional (3-D) model based on a real clinical coronary artery and analysed the optimal stenting strategies by computational simulation. Via microfabrication and 3-D printing technology, the digital model was also converted into in vitro microfluidic models with 3-D micro channels. Simultaneously, physicians placed real stents inside them; i.e., they performed "virtual surgeries". The hydrodynamic experimental results showed that the microfluidic models highly inosculated the simulations. Therefore, our study not only demonstrated that the half-cross stenting strategy could maximally reduce restenosis risks but also indicated that 3-D printing combined with clinical image reconstruction is a promising method for future angiocardiopathy research. PMID:26042609

  1. Challenging Issues on fog forecast with a three-dimensional fog forecast model

    NASA Astrophysics Data System (ADS)

    Masbou, M.

    2012-12-01

    Fog has a significant impact on economical aspect (traffic management and safety) as well as on environmental issues (fresh water source for the population and the biosphere in arid region). However, reliable fog and visibility forecasts stay challenging issue. Fog is generally a small scale phenomenon which is mostly affected by local advective transport, radiation, topography, vegetation, turbulent mixing at the surface as well as its microphysical structure. In order to consider these intertwined processes, the three-dimensional fog forecast model, COSMO-FOG, with a high vertical resolution with different microphysical complexity has been developed. This model includes a microphysical parameterisation based on the one-dimensional fog forecast model. The implementation of the cloud water droplets as a new prognostic variable allows a detailed definition of the sedimentation processes and the variations in visibility. Moreover, the turbulence scheme, based on a Mellor-Yamada 2.5 order and a closure of a 2nd order has been modified to improve the model behaviour in case of a stable atmosphere structure, occurring typically during night radiative fog episodes. The potential of COSMO-FOG will be presented in some realistic fog situations (flat, bumpy and complex terrain). The fog spatial extension will be compared with MSG satellite products for fog and low cloud. The interplays between dynamical, thermodynamical patterns and the soil-atmosphere interactions will be presented.

  2. A Three-Dimensional Finite Element Model of the Radiocarpal Joint

    PubMed Central

    Anderson, Donald D; Deshpande, Balachandra R; Daniel, Thomas E; Baratz, Mark E

    2005-01-01

    Displaced intra-articular distal radius fractures are difficult to treat, with numerous associated complications. The potential onset of post-traumatic osteoarthritis (OA) is a major concern. The relationship between malreduced intra-articular fracture of the distal radius and subsequent early onset of radiocarpal OA is clinically important, yet poorly understood. To better understand this presumed mechanical relationship, detailed information regarding joint loading, kinematics and associated stress distributions must be obtained. Toward this end, a three-dimensional finite element (3D FE) contact model of the radiocarpal joint has been developed, including the radius, lunate, scaphoid, articulations between these bones and selected soft tissues near the joint. FE model geometry was derived from cryomicrotome sections of a cadaver wrist. Radiocarpal contact stress distributions in the intact and simulated malreduced fracture conditions, previously collected using a cadaveric intra-articular fracture model, are used to establish validity of the computational model. Finally, a section of the distal radius constituting the entire lunate fossa was displaced 1, 2 and 3 mm to represent a depressed lunate die-punch fracture. PMID:16089082

  3. Three-dimensional virtual surgery models for percutaneous coronary intervention (PCI) optimization strategies

    PubMed Central

    Wang, Hujun; Liu, Jinghua; Zheng, Xu; Rong, Xiaohui; Zheng, Xuwei; Peng, Hongyu; Silber-Li, Zhanghua; Li, Mujun; Liu, Liyu

    2015-01-01

    Percutaneous coronary intervention (PCI), especially coronary stent implantation, has been shown to be an effective treatment for coronary artery disease. However, in-stent restenosis is one of the longstanding unsolvable problems following PCI. Although stents implanted inside narrowed vessels recover normal flux of blood flows, they instantaneously change the wall shear stress (WSS) distribution on the vessel surface. Improper stent implantation positions bring high possibilities of restenosis as it enlarges the low WSS regions and subsequently stimulates more epithelial cell outgrowth on vessel walls. To optimize the stent position for lowering the risk of restenosis, we successfully established a digital three-dimensional (3-D) model based on a real clinical coronary artery and analysed the optimal stenting strategies by computational simulation. Via microfabrication and 3-D printing technology, the digital model was also converted into in vitro microfluidic models with 3-D micro channels. Simultaneously, physicians placed real stents inside them; i.e., they performed “virtual surgeries”. The hydrodynamic experimental results showed that the microfluidic models highly inosculated the simulations. Therefore, our study not only demonstrated that the half-cross stenting strategy could maximally reduce restenosis risks but also indicated that 3-D printing combined with clinical image reconstruction is a promising method for future angiocardiopathy research. PMID:26042609

  4. A three-dimensional gravity model of the geologic structure of Long Valley caldera

    SciTech Connect

    Carle, S.F.; Goldstein, N.E.

    1987-03-01

    Several attempts to define and interpret this anomaly have been made in the past using 2-D and 3-D models. None of the previous interpretations have yielded definitive results, but in fairness, the interpretation here has benefited from a larger gravity data base and more subsurface control than available to previous workers. All published 3-D models simplistically assumed constant density of fill. All 2-D models suffered from the inherent three-dimensionality of the complicated density structure of Long Valley caldera. In addition, previous interpreters have lacked access to geological data, such as well lithologies and density logs, seismic refraction interpretations, suface geology, and structural geology interpretations. The purpose of this study is to use all available gravity data and geological information to constrain a multi-unit, 3-D density model based on the geology of Long Valley caldera and its vicinity. Insights on the geologic structure of the caldera fill can help other geophysical interpretations in determining near-surface effects so that deeper structure may be resolved. With adequate control on the structure of the caldera fill, we are able to examine the gravity data for the presence of deeper density anomalies in the crust. 20 refs., 7 figs.

  5. Engineering of microscale three-dimensional pancreatic islet models in vitro and their biomedical applications.

    PubMed

    Gao, Bin; Wang, Lin; Han, Shuang; Pingguan-Murphy, Belinda; Zhang, Xiaohui; Xu, Feng

    2016-08-01

    Diabetes now is the most common chronic disease in the world inducing heavy burden for the people's health. Based on this, diabetes research such as islet function has become a hot topic in medical institutes of the world. Today, in medical institutes, the conventional experiment platform in vitro is monolayer cell culture. However, with the development of micro- and nano-technologies, several microengineering methods have been developed to fabricate three-dimensional (3D) islet models in vitro which can better mimic the islet of pancreases in vivo. These in vitro islet models have shown better cell function than monolayer cells, indicating their great potential as better experimental platforms to elucidate islet behaviors under both physiological and pathological conditions, such as the molecular mechanisms of diabetes and clinical islet transplantation. In this review, we present the state-of-the-art advances in the microengineering methods for fabricating microscale islet models in vitro. We hope this will help researchers to better understand the progress in the engineering 3D islet models and their biomedical applications such as drug screening and islet transplantation.

  6. Coupled Plasticity and Damage Modeling and Their Applications in a Three-Dimensional Eulerian Hydrocode

    NASA Astrophysics Data System (ADS)

    Burkett, Michael W.; Clancy, Sean P.; Maudlin, Paul J.; Holian, Kathleen S.

    2004-07-01

    Previously developed constitutive models and solution algorithms for continuum-level anisotropic elastoplastic material strength and an isotropic damage model TEPLA have been implemented in the three-dimensional Eulerian hydrodynamics code known as CONEJO. The anisotropic constitutive modeling is posed in an unrotated material frame of reference using the theorem of polar decomposition to compute rigid-body rotation. TEPLA is based upon the Gurson flow surface (a potential function used in conjunction with the associated flow law). The original TEPLA equation set has been extended to include anisotropic elastoplasticity and has been recast into a new implicit solution algorithm based upon an eigenvalue scheme to accommodate the anisotropy. This algorithm solves a two-by-two system of nonlinear equations using a Newton-Raphson iteration scheme. Simulations of a shaped-charge jet formation, a Taylor cylinder impact, and an explosively loaded hemishell were selected to demonstrate the utility of this modeling capability. The predicted deformation topology, plastic strain, and porosity distributions are shown for the three simulations.

  7. 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.

  8. Simulating Water Flow in Variably Saturated Soils - Exploring the Advantage of Three-dimensional Models

    NASA Astrophysics Data System (ADS)

    Hopp, L.; Ivanov, V. Y.

    2010-12-01

    There is still a debate in rainfall-runoff modeling over the advantage of using three-dimensional models based on partial differential equations describing variably saturated flow vs. models with simpler infiltration and flow routing algorithms. Fully explicit 3D models are computationally demanding but allow the representation of spatially complex domains, heterogeneous soils, conditions of ponded infiltration, and solute transport, among others. Models with simpler infiltration and flow routing algorithms provide faster run times and are likely to be more versatile in the treatment of extreme conditions such as soil drying but suffer from underlying assumptions and ad-hoc parameterizations. In this numerical study, we explore the question of whether these two model strategies are competing approaches or if they complement each other. As a 3D physics-based model we use HYDRUS-3D, a finite element model that numerically solves the Richards equation for variably-saturated water flow. As an example of a simpler model, we use tRIBS+VEGGIE that solves the 1D Richards equation for vertical flow and applies Dupuit-Forchheimer approximation for saturated lateral exchange and gravity-driven flow for unsaturated lateral exchange. The flow can be routed using either the D-8 (steepest descent) or D-infinity flow routing algorithms. We study lateral subsurface stormflow and moisture dynamics at the hillslope-scale, using a zero-order basin topography, as a function of storm size, antecedent moisture conditions and slope angle. The domain and soil characteristics are representative of a forested hillslope with conductive soils in a humid environment, where the major runoff generating process is lateral subsurface stormflow. We compare spatially integrated lateral subsurface flow at the downslope boundary as well as spatial patterns of soil moisture. We illustrate situations where both model approaches perform equally well and identify conditions under which the application of a

  9. A three-dimensional musculoskeletal model of the chimpanzee (Pan troglodytes) pelvis and hind limb.

    PubMed

    O'Neill, Matthew C; Lee, Leng-Feng; Larson, Susan G; Demes, Brigitte; Stern, Jack T; Umberger, Brian R

    2013-10-01

    Musculoskeletal models have become important tools for studying a range of muscle-driven movements. However, most work has been in modern humans, with few applications in other species. Chimpanzees are facultative bipeds and our closest living relatives, and have provided numerous important insights into our own evolution. A chimpanzee musculoskeletal model would allow integration across a wide range of laboratory-based experimental data, providing new insights into the determinants of their locomotor performance capabilities, as well as the origins and evolution of human bipedalism. Here, we described a detailed three-dimensional (3D) musculoskeletal model of the chimpanzee pelvis and hind limb. The model includes geometric representations of bones and joints, as well as 35 muscle-tendon units that were represented using 44 Hill-type muscle models. Muscle architecture data, such as muscle masses, fascicle lengths and pennation angles, were drawn from literature sources. The model permits calculation of 3D muscle moment arms, muscle-tendon lengths and isometric muscle forces over a wide range of joint positions. Muscle-tendon moment arms predicted by the model were generally in good agreement with tendon-excursion estimates from cadaveric specimens. Sensitivity analyses provided information on the parameters that model predictions are most and least sensitive to, which offers important context for interpreting future results obtained with the model. Comparisons with a similar human musculoskeletal model indicate that chimpanzees are better suited for force production over a larger range of joint positions than humans. This study represents an important step in understanding the integrated function of the neuromusculoskeletal systems in chimpanzee locomotion. PMID:24006347

  10. A three-dimensional musculoskeletal model of the chimpanzee (Pan troglodytes) pelvis and hind limb.

    PubMed

    O'Neill, Matthew C; Lee, Leng-Feng; Larson, Susan G; Demes, Brigitte; Stern, Jack T; Umberger, Brian R

    2013-10-01

    Musculoskeletal models have become important tools for studying a range of muscle-driven movements. However, most work has been in modern humans, with few applications in other species. Chimpanzees are facultative bipeds and our closest living relatives, and have provided numerous important insights into our own evolution. A chimpanzee musculoskeletal model would allow integration across a wide range of laboratory-based experimental data, providing new insights into the determinants of their locomotor performance capabilities, as well as the origins and evolution of human bipedalism. Here, we described a detailed three-dimensional (3D) musculoskeletal model of the chimpanzee pelvis and hind limb. The model includes geometric representations of bones and joints, as well as 35 muscle-tendon units that were represented using 44 Hill-type muscle models. Muscle architecture data, such as muscle masses, fascicle lengths and pennation angles, were drawn from literature sources. The model permits calculation of 3D muscle moment arms, muscle-tendon lengths and isometric muscle forces over a wide range of joint positions. Muscle-tendon moment arms predicted by the model were generally in good agreement with tendon-excursion estimates from cadaveric specimens. Sensitivity analyses provided information on the parameters that model predictions are most and least sensitive to, which offers important context for interpreting future results obtained with the model. Comparisons with a similar human musculoskeletal model indicate that chimpanzees are better suited for force production over a larger range of joint positions than humans. This study represents an important step in understanding the integrated function of the neuromusculoskeletal systems in chimpanzee locomotion.

  11. Evaluation of dynamical parameters with a three-dimensional mechanistic model of the middle atmosphere

    SciTech Connect

    Kouker, W.

    1993-12-01

    A three-dimensional model of the middle atmosphere is introduced. The model is based on the full set of the primitive equations. It is designed to simulate a yearly cycle of the middle atmosphere. Results are presented for the solstice and equinox conditions. The model reproduces the main observed features of the middle atmospheric circulation: the stratospheric-mesospheric jet streams and the cold summer mesopause region at solstice with reversed zonal wind especially in the summer mesosphere, and the weak westerly circulation at equinox. The parameterized effects of breaking gravity waves in the mesosphere drive the atmosphere out of radiative balance. They lead to a meridional circulation with a one-cell structure at solstice with upward (downward) motion over the summer (winter) pole and a meridional flow towards the winter hemisphere and a two-cell structure at equinox with upward motion over the tropics and downward motion over the polar regions. Potential fields are presented for horizontal vector fields. They suggest that the stratospheric circulation can is dominated by horizontally nondivergent flow. This is modified by the results of a more quantitative view at the interaction of planetary waves on the zonal mean flow, which clearly identifies the essential role of horizontal divergence on the stratospheric circulation.

  12. A three-dimensional model of primary bovine endometrium using an electrospun scaffold.

    PubMed

    MacKintosh, S B; Serino, L P; Iddon, P D; Brown, R; Conlan, R S; Wright, C J; Maffeis, T G G; Raxworthy, M J; Sheldon, I M

    2015-06-01

    Endometrial stromal and epithelial cell function is typically studied in vitro using standard two-dimensional monocultures, but these cultures fail to reflect the complex three-dimensional (3D) architecture of tissue. A 3D model of bovine endometrium that reflects the architectural arrangement of in vivo tissue would beneficially assist the study of tissue function. An electrospun polyglycolide (PGA) scaffold was selected to grow a 3D model of primary bovine endometrial epithelial and stromal cells, that reflects the architecture of the endometrium for the study of pathophysiology. Electrospun scaffolds were seeded with stromal and epithelial cells, and growth was assessed using histological techniques. Prostaglandin E2 and prostaglandin F2α responsiveness of endometrial scaffold constructs was tested using oxytocin plus arachidonic acid (OT + AA) or lipopolysaccharide (LPS). Stromal and epithelial cells growing on the electrospun scaffold had an architectural arrangement that mimicked whole tissue, deposited fibronectin, had appropriate expression of vimentin and cytokeratin and were responsive to OT + AA and LPS, as measured by prostaglandin accumulation. In conclusion, a functional 3D model of stromal and epithelial cells was developed using a PGA electrospun scaffold which may be used to study endometrial pathophysiology.

  13. Dynamical response of the atmosphere to energetic particles: three-dimensional model simulations

    NASA Astrophysics Data System (ADS)

    Krivolutsky, A.; Vyushkova, T.; Kuminov, A.; Zakharov, G.; Klyuchnikova, A.

    3D middle atmosphere general circulation model, and chemical global transport model have been used to calculate the response of ozone (and other species), wind and temperature regime after two strongest solar proton events (SPEs) of 23rd solar cycle. These events occurred in July 2000 and October 2003. It was assumed in photochemical scheme that each pair of ions created at high latitude middle atmosphere by solar energetic protons born approximately one molecular of NO and two molecular of OH, which disturb photochemical system in the stratosphere and mesosphere. Ionization rates caused by SPE has been calculated using high time-resolution satellite measurements of solar proton fluxes from the board of satellite GOES-10. 3D photochemical calculations showed that ozone was strongly reduced in the mesosphere region (about 60-70 % with minus), but corresponding "tail" of disturbances existed more than 10 days after SPEs due to the enhancement of long-lived NOx . The results of numerical photochemical simulations of ozone depletion after SPEs has been introduced into three-dimensional model of general circulation of the middle atmosphere, and showed that such ozone depletion leads to the disturbances in atmospheric temperature and wind regimes. It was also shown that the response of temperature and wind fields is very steady in time So, we must take it into account looking for mechanisms of global change and climate variability. This work was supported by Russian Science Foundation (grant number: 03-05-64675).

  14. Cytopede: A Three-Dimensional Tool for Modeling Cell Motility on a Flat Surface

    PubMed Central

    Dembo, Micah

    2010-01-01

    Abstract When cultured on flat surfaces, fibroblasts and many other cells spread to form thin lamellar sheets. Motion then occurs by extension of the sheet at the leading edge and retraction at the trailing edge. Comprehensive quantitative models of these phenomena have so far been lacking and to address this need, we have designed a three-dimensional code called Cytopede specialized for the simulation of the mechanical and signaling behavior of plated cells. Under assumptions by which the cytosol and the cytoskeleton are treated from a continuum mechanical perspective, Cytopede uses the finite element method to solve mass and momentum equations for each phase, and thus determine the time evolution of cellular models. We present the physical concepts that underlie Cytopede together with the algorithms used for their implementation. We then validate the approach by a computation of the spread of a viscous sessile droplet. Finally, to exemplify how Cytopede enables the testing of ideas about cell mechanics, we simulate a simple fibroblast model. We show how Cytopede allows computation, not only of basic characteristics of shape and velocity, but also of maps of cell thickness, cytoskeletal density, cytoskeletal flow, and substratum tractions that are readily compared with experimental data. PMID:20958108

  15. Three-Dimensional Modeling of the Solar Wind: From the Coronal Base to the Outer Heliosphere

    NASA Technical Reports Server (NTRS)

    Usmanov, A. V; Goldstein, M. L.; Matthaeus, W. H.

    2011-01-01

    We have developed a global fully three-dimensional magnetohydrodynamic solar wind model for the region that extends from the coronal base to 100 AU. The simulation domain consists of tree spherical shell subdomains with computational boundaries between them placed at 20 solar radii and 0.3 AU. The location of the first boundary ensures that the flow at the boundary is both supersonic and super-Alfvenic. A steady-state solution in the innermost (coronal) region is obtained by the time-relaxation method. The solution uses a tilted dipole model or solar magnetograms as the boundary condition at the coronal base and includes a flux of Alfven waves in the WKB approximation which provide additional acceleration for the coronal outflow in the open field regions. The intermediate region solution is constructed by the integration of steady-state equations along radius using a marching scheme. The outer region solution (0.3-100 AU) is obtained again by the time relaxation and takes into account turbulence transport and heating as well as heating, flow deceleration, and other effects due to the interstellar pickup protons treated as a separate fluid. We use the model to simulate the global steady-state structure of the solar wind from the coronal base to the heliospheric boundary and compare the results with Ulysses and Voyager observations.

  16. Modeling and numerical analysis of compression molding of three-dimensional thin parts with curing process

    SciTech Connect

    Kwon, T.H.; Kim, C.S.

    1995-07-01

    A numerical modeling is proposed for the simulation of flow, heat transfer, and reaction kinetics during the compression molding of three-dimensional thin parts. A nonisothermal, non-Newtonian model including the kinetic equation for a curing mechanism of thermosetting materials is implemented in a computer program, and a finite element method is used to simulate a preheating, a filling, and a post-heating stage during the entire compression molding process. As a more rigorous approach, a moving boundary condition due to the drag motion of an upper mold of a nonplanar shape or due to an apparent slip phenomena of particle filled materials is introduced into the present modeling, resulting in a new governing equation and the corresponding finite element formulation. Verifications of the analysis program were performed with a simple geometry for the Newtonian and non-Newtonian isothermal cases, in which the numerical results are found to be in good agreement with theoretical results. Effects of the moving boundary condition and processing conditions, such as thickness of compression molded parts, mold closing velocity and the preheating stage on overall compression molding processing, are numerically investigated.

  17. Renormalization, duality, and phase transitions in two- and three-dimensional quantum dimer models

    SciTech Connect

    Nogueira, Flavio S.; Nussinov, Zohar

    2009-09-01

    We derive an extended lattice gauge theory type action for quantum dimer models and relate it to the height representations of these systems. We examine the system in two and three dimensions and analyze the phase structure in terms of effective theories and duality arguments. For the two-dimensional case we derive the effective potential both at zero and finite temperature. The zero-temperature theory at the Rokhsar-Kivelson (RK) point has a critical point related to the self-dual point of a class of Z{sub N} models in the N{yields}{infinity} limit. Two phase transitions featuring a fixed line are shown to appear in the phase diagram, one at zero temperature and at the RK point and another one at finite temperature above the RK point. The latter will be shown to correspond to a Kosterlitz-Thouless (KT) phase transition, while the former will be governed by a KT-like universality class, i.e., sharing many features with a KT transition but actually corresponding to a different universality class. On the other hand, we show that at the RK point no phase transition happens at finite temperature. For the three-dimensional case we derive the corresponding dual gauge theory model at the RK point. We show in this case that at zero temperature a first-order phase transition occurs, while at finite temperatures both first- and second-order phase transitions are possible, depending on the relative values of the couplings involved.

  18. Three-dimensional time-dependent computer modeling of the electrothermal atomizers for analytical spectrometry

    NASA Astrophysics Data System (ADS)

    Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.

    2016-02-01

    A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.

  19. Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers

    NASA Technical Reports Server (NTRS)

    Snyder, Aaron; Banks, Bruce A.

    2002-01-01

    A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.

  20. Three-dimensional modeling of diesel engine intake flow, combustion and emissions

    NASA Technical Reports Server (NTRS)

    Reitz, R. D.; Rutland, C. J.

    1992-01-01

    A three-dimensional computer code (KIVA) is being modified to include state-of-the-art submodels for diesel engine flow and combustion: spray atomization, drop breakup/coalescence, multi-component fuel vaporization, spray/wall interaction, ignition and combustion, wall heat transfer, unburned HC and NOx formation, soot and radiation, and the intake flow process. Improved and/or new submodels which were completed are: wall heat transfer with unsteadiness and compressibility, laminar-turbulent characteristic time combustion with unburned HC and Zeldo'vich NOx, and spray/wall impingement with rebounding and sliding drops. Results to date show that adding the effects of unsteadiness and compressibility improves the accuracy of heat transfer predictions; spray drop rebound can occur from walls at low impingement velocities (e.g., in cold-starting); larger spray drops are formed at the nozzle due to the influence of vaporization on the atomization process; a laminar-and-turbulent characteristic time combustion model has the flexibility to match measured engine combustion data over a wide range of operating conditions; and finally, the characteristic time combustion model can also be extended to allow predictions of ignition. The accuracy of the predictions is being assessed by comparisons with available measurements. Additional supporting experiments are also described briefly. To date, comparisons with measured engine cylinder pressure and heat flux data were made for homogeneous charge, spark-ignited and compression-ignited engines. The model results are in good agreement with the experiments.

  1. End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

    PubMed Central

    Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G.

    2016-01-01

    Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis. PMID:26901845

  2. The design, construction and three dimensional modeling of a high pressure organometallic chemical vapor deposition reactor

    NASA Astrophysics Data System (ADS)

    McCall, Sonya Denise

    Two high pressure reactors have been designed, built and tested, in order to extend Organometallic Chemical Vapor Deposition (OMCVD) to materials that exhibit large thermal decomposition pressures at their optimum growth temperature. The Differentially Pressure Controlled (DPC) Reactor System was designed and built for use at pressures ≤10 atm. A second generation reactor, the Compact Hard Shell (CHS) Reactor was built in order to extend pressures ≤100 atm. A physico-chemical model of the High Pressure Organometallic Chemical Vapor Deposition (HPOMCVD) process that describes three dimensional transport phenomena as well as gas-phase and surface reactions underlying the growth of compound semiconductors is presented. A reduced-order model of the Organometallic Chemical Vapor Deposition of InN from trimethylindium and ammonia at elevated pressures has been developed and tested. The model describes the flow dynamics coupled to chemical reactions and transport in the flow channel of the Compact Hard Shell Reactor, as a function of substrate temperature, total pressure and centerline flow velocity.

  3. Beam model and three dimensional numerical simulations on suspended microchannel resonators

    NASA Astrophysics Data System (ADS)

    Huang, Kuan-Rong; Chang, Jeng-Shian; Chao, Sheng D.; Wu, Kuang-Chong

    2012-12-01

    At the microscale level, the vibrational characteristics of microstructures have been widely applied on biochemical microchips, especially for bio-molecules detection. The vibrational mechanics and mechanism of microcantilever beams immersed in the fluids for detecting target bio-molecules carried in the fluids have been widely studied and realized in recent years. However, it is not the case for microcantilever beams containing fluids inside (called suspended microchannel resonators, SMR). In this paper, an 1-D beam model for SMR is proposed and the formula for prediction of resonant frequency and resonant frequency shift are derived. For verification of validity of the 1-D beam model, three dimensional finite element simulations using ANSYS are performed. The effects of relevant parameters, such as density and viscosity of the fluids, on the frequency response are investigated. A link between numerical simulations and mathematical modeling is established through an equivalence relation. Subsequently, a useful formula of the resonant frequency shift as a function of the mass variation and the viscosity of the contained fluid is derived. Good agreement between the numerical simulations and the experimental data is obtained and the physical mechanism is elucidated.

  4. End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites.

    PubMed

    Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G

    2016-01-01

    Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis. PMID:26901845

  5. Vacuum modeling of three-dimensional magnetic field topology under resonant magnetic perturbations on EAST

    NASA Astrophysics Data System (ADS)

    Jia, M.; Sun, Y.; Zhong, F.; Li, H.; Li, G.; Wang, L.; Gan, K.; Zhang, B.; Qian, J.; Shen, B.

    2016-05-01

    A numerical model using field line tracing for modeling of three-dimensional magnetic field topology under resonant magnetic perturbations (RMPs) on experimental advanced superconducting tokamak (EAST) is presented. The topological structure is calculated in the vacuum paradigm. The modeling result predicts that the possible strike point splitting on a plasma-facing component and the lobes-like structure on the boundary are observable in the diagnostics at different locations. It is shown that the magnetic perturbations with a resonant dominant spectrum can induce a large footprint splitting effect as well as a wide stochastic layer. This is useful for observations using diagnostics with limited spatial resolution. The impact of RMP fields on marginally disconnected double null configurations is investigated. To avoid the transient heat load on the upper divertor or plasma-facing components near the upper x-point, it is necessary to keep the distance between two separatrices of a near double null configuration larger than a threshold value that depends on the RMP strength and the equilibrium properties. A preliminary RMP experiment on EAST shows that there is a good agreement between the splitting width predicted by the code and that of the particle flux measured by divertor probes. An enhancement of particle flux on the upper divertor during the RMP phase is observed in the lower single null discharge.

  6. Perceptual disturbances predicted in zero-g through three-dimensional modeling.

    PubMed

    Holly, Jan E

    2003-01-01

    Perceptual disturbances in zero-g and 1-g differ. For example, the vestibular coriolis (or "cross-coupled") effect is weaker in zero-g. In 1-g, blindfolded subjects rotating on-axis experience perceptual disturbances upon head tilt, but the effects diminish in zero-g. Head tilts during centrifugation in zero-g and 1-g are investigated here by means of three-dimensional modeling, using a model that was previously used to explain the zero-g reduction of the on-axis vestibular coriolis effect. The model's foundation comprises the laws of physics, including linear-angular interactions in three dimensions. Addressed is the question: In zero-g, will the vestibular coriolis effect be as weak during centrifugation as during on-axis rotation? Centrifugation in 1-g was simulated first, with the subject supine, head toward center. The most noticeable result concerned direction of head yaw. For clockwise centrifuge rotation, greater perceptual effects arose in simulations during yaw counterclockwise (as viewed from the top of the head) than for yaw clockwise. Centrifugation in zero-g was then simulated with the same "supine" orientation. The result: In zero-g the simulated vestibular coriolis effect was greater during centrifugation than during on-axis rotation. In addition, clockwise-counterclockwise differences did not appear in zero-g, in contrast to the differences that appear in 1-g.

  7. Effects of using two- versus three-dimensional computational modeling of fluidized beds Part I, hydrodynamics

    SciTech Connect

    Xie, Nan; Battaglia, Francine; Pannala, Sreekanth

    2008-01-01

    Simulations of fluidized beds are performed to study and determine the effect on the use of coordinate systems and geometrical configurations to model fluidized bed reactors. Computational fluid dynamics is employed for an Eulerian-Eulerian model, which represents each phase as an interspersed continuum. The transport equation for granular temperature is solved and a hyperbolic tangent function is used to provide a smooth transition between the plastic and viscous regimes for the solid phase. The aim of the present work is to show the range of validity for employing simulations based on a 2D Cartesian coordinate system to approximate both cylindrical and rectangular fluidized beds. Three different fluidization regimes, bubbling, slugging and turbulent regimes, are investigated and the results of 2D and 3D simulations are presented for both cylindrical and rectangular domains. The results demonstrate that a 2D Cartesian system can be used to successfully simulate and predict a bubbling regime. However, caution must be exercised when using 2D Cartesian coordinates for other fluidized regimes. A budget analysis that explains all the differences in detail is presented in Part II [N. Xie, F. Battaglia, S. Pannala, Effects of Using Two-Versus Three-Dimensional Computational Modeling of Fluidized Beds: Part II, budget analysis, 182 (1) (2007) 14] to complement the hydrodynamic theory of this paper.

  8. In vitro three-dimensional cancer metastasis modeling: Past, present, and future

    NASA Astrophysics Data System (ADS)

    Wei-jing, Han; Wei, Yuan; Jiang-rui, Zhu; Qihui, Fan; Junle, Qu; Li-yu, Liu

    2016-01-01

    Metastasis is the leading cause of most cancer deaths, as opposed to dysregulated cell growth of the primary tumor. Molecular mechanisms of metastasis have been studied for decades and the findings have evolved our understanding of the progression of malignancy. However, most of the molecular mechanisms fail to address the causes of cancer and its evolutionary origin, demonstrating an inability to find a solution for complete cure of cancer. After being a neglected area of tumor biology for quite some time, recently several studies have focused on the impact of the tumor microenvironment on cancer growth. The importance of the tumor microenvironment is gradually gaining attention, particularly from the perspective of biophysics. In vitro three-dimensional (3-D) metastatic models are an indispensable platform for investigating the tumor microenvironment, as they mimic the in vivo tumor tissue. In 3-D metastatic in vitro models, static factors such as the mechanical properties, biochemical factors, as well as dynamic factors such as cell-cell, cell-ECM interactions, and fluid shear stress can be studied quantitatively. With increasing focus on basic cancer research and drug development, the in vitro 3-D models offer unique advantages in fundamental and clinical biomedical studies. Project supported by the National Basic Research Program of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345), and the Beijing Natural Science Foundation, China (Grant No. 7154221).

  9. Perceptual disturbances predicted in zero-g through three-dimensional modeling.

    PubMed

    Holly, Jan E

    2003-01-01

    Perceptual disturbances in zero-g and 1-g differ. For example, the vestibular coriolis (or "cross-coupled") effect is weaker in zero-g. In 1-g, blindfolded subjects rotating on-axis experience perceptual disturbances upon head tilt, but the effects diminish in zero-g. Head tilts during centrifugation in zero-g and 1-g are investigated here by means of three-dimensional modeling, using a model that was previously used to explain the zero-g reduction of the on-axis vestibular coriolis effect. The model's foundation comprises the laws of physics, including linear-angular interactions in three dimensions. Addressed is the question: In zero-g, will the vestibular coriolis effect be as weak during centrifugation as during on-axis rotation? Centrifugation in 1-g was simulated first, with the subject supine, head toward center. The most noticeable result concerned direction of head yaw. For clockwise centrifuge rotation, greater perceptual effects arose in simulations during yaw counterclockwise (as viewed from the top of the head) than for yaw clockwise. Centrifugation in zero-g was then simulated with the same "supine" orientation. The result: In zero-g the simulated vestibular coriolis effect was greater during centrifugation than during on-axis rotation. In addition, clockwise-counterclockwise differences did not appear in zero-g, in contrast to the differences that appear in 1-g. PMID:15096662

  10. Three-dimensional model on thermal response of skin subject to laser heating.

    PubMed

    Shen, Wensheng; Zhang, Jun; Yang, Fuqian

    2005-04-01

    A three-dimensional (3D) multilayer model based on the skin physical structure is developed to investigate the transient thermal response of human skin subject to laser heating. The temperature distribution of the skin is modeled by the bioheat transfer equation, and the influence of laser heating is expressed as a source term where the strength of the source is a product of a Gaussian shaped incident irradiance, an exponentially shaped axial attenuation, and a time function. The water evaporation and diffusion is included in the model by adding two terms regarding the heat loss due to the evaporation and diffusion, where the rate of water evaporation is determined based on the theory of laminar boundary layer. Cryogen spray cooling (CSC) in laser therapy is studied, as well as its effect on the skin thermal response. The time-dependent equation is discretized using the finite difference method with the Crank-Nicholson scheme and the stability of the numerical method is analyzed. The large sparse linear system resulted from discretizing the governing partial differential equation is solved by a GMRES solver and the expected simulation results are obtained.

  11. Measurement and modeling of three-dimensional equilibria in DIII-D

    SciTech Connect

    Lanctot, M. J.; Reimerdes, H.; Navratil, G. A.; Garofalo, A. M.; Chu, M. S.; Jackson, G. L.; La Haye, R. J.; Schaffer, M. J.; Strait, E. J.; Turnbull, A. D.; Hanson, J. M.; Liu, Y. Q.; Okayabashi, M.; Park, J.-K.; Schmitz, O.

    2011-05-15

    A detailed experiment-theory comparison reveals that linear ideal MHD theory is in quantitative agreement with external magnetic and internal soft x-ray measurements of the plasma response to externally applied non-axisymmetric fields over a broad range of beta and rotation. This result represents a significant step toward the goal of advancing the understanding of three-dimensional tokamak equilibria. Both the magnetic and soft x-ray measurements show the driven plasma perturbation increases linearly with the applied perturbation, suggesting the relevance of linear plasma response models. The magnetic and soft x-ray measurements are made at multiple toroidal and poloidal locations, allowing well resolved measurements of the global structure. The comparison also highlights the need to include kinetic effects in the MHD model once beta exceeds 80% of the kink mode limit without a conducting wall. Two distinct types of response fields are identified by the linear ideal MHD model: one that consists of localized currents at the rational surfaces that cancel the applied resonant field and another that is excited by the components of the external field that couple to the kink mode. Numerical simulations show these two fields have similar amplitudes in ITER-shaped DIII-D discharges where n = 3 fields are used to suppress edge localized modes.

  12. A phasor approach analysis of multiphoton FLIM measurements of three-dimensional cell culture models

    NASA Astrophysics Data System (ADS)

    Lakner, P. H.; Möller, Y.; Olayioye, M. A.; Brucker, S. Y.; Schenke-Layland, K.; Monaghan, M. G.

    2016-03-01

    Fluorescence lifetime imaging microscopy (FLIM) is a useful approach to obtain information regarding the endogenous fluorophores present in biological samples. The concise evaluation of FLIM data requires the use of robust mathematical algorithms. In this study, we developed a user-friendly phasor approach for analyzing FLIM data and applied this method on three-dimensional (3D) Caco-2 models of polarized epithelial luminal cysts in a supporting extracellular matrix environment. These Caco-2 based models were treated with epidermal growth factor (EGF), to stimulate proliferation in order to determine if FLIM could detect such a change in cell behavior. Autofluorescence from nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) in luminal Caco-2 cysts was stimulated by 2-photon laser excitation. Using a phasor approach, the lifetimes of involved fluorophores and their contribution were calculated with fewer initial assumptions when compared to multiexponential decay fitting. The phasor approach simplified FLIM data analysis, making it an interesting tool for non-experts in numerical data analysis. We observed that an increased proliferation stimulated by EGF led to a significant shift in fluorescence lifetime and a significant alteration of the phasor data shape. Our data demonstrates that multiphoton FLIM analysis with the phasor approach is a suitable method for the non-invasive analysis of 3D in vitro cell culture models qualifying this method for monitoring basic cellular features and the effect of external factors.

  13. Three-dimensional micromechanical models for the nonlinear analysis of pultruded composite structures

    NASA Astrophysics Data System (ADS)

    Kilic, Mustafa Hakan

    This study presents a new three-dimensional (3D) micromechanics-based nonlinear framework for the analysis of pultruded composite structures. The proposed material modeling framework is a nested micromechanical approach that explicitly recognizes the different composite systems within the cross-section of a pultruded composite member. The 3D lamination theory is used to generate a homogenized nonlinear effective response using a through-thickness representative stacking sequence. Different 3D micromechanical models can be used to represent the composite layers within the repeating stacking sequence, e.g. roving layer, continuous filament mat (CFM), and woven fabrics. The proposed modeling framework is applied for pultruded composite material systems made from roving and CFM. The roving layer is idealized using an existing 3D nonlinear micromechanics model for a unidirectional fiber reinforced material. A simple nonlinear micromechanical model for the CFM layer is introduced and implemented. The overall modeling approach is able to predict both the elastic and nonlinear response of the composite material based on the in-situ properties and response of the fiber and matrix constituents. Experimental data, from off-axis tests of pultruded plates, is used to verify the proposed modeling approach. The 3D modeling framework shows good prediction capabilities for the overall effective elastic constants, as well as the nonlinear multi-axial stress-strain response. In addition, a simple degradation and damage modeling is coupled with the proposed analysis framework. Several applications are performed for the nonlinear analysis of pultruded composite structures, such as progressive failure analysis of notched plates, bending of short beams, and damage analysis of pultruded FRP bolted connections.

  14. Development of a Three-Dimensional Finite Element Chest Model for the 5(th) Percentile Female.

    PubMed

    Kimpara, Hideyuki; Lee, Jong B; Yang, King H; King, Albert I; Iwamoto, Masami; Watanabe, Isao; Miki, Kazuo

    2005-11-01

    Several three-dimensional (3D) finite element (FE) models of the human body have been developed to elucidate injury mechanisms due to automotive crashes. However, these models are mainly focused on 50(th) percentile male. As a first step towards a better understanding of injury biomechanics in the small female, a 3D FE model of a 5(th) percentile female human chest (FEM-5F) has been developed and validated against experimental data obtained from two sets of frontal impact, one set of lateral impact, two sets of oblique impact and a series of ballistic impacts. Two previous FE models, a small female Total HUman Model for Safety (THUMS-AF05) occupant version 1.0Beta (Kimpara et al. 2002) and the Wayne State University Human Thoracic Model (WSUHTM, Wang 1995 and Shah et al. 2001) were integrated and modified for this model development. The model incorporated not only geometrical gender differences, such as location of the internal organs and structure of the bony skeleton, but also the biomechanical differences of the ribs due to gender. It includes a detailed description of the sternum, ribs, costal cartilage, thoracic spine, skin, superficial muscles, intercostal muscles, heart, lung, diaphragm, major blood vessels and simplified abdominal internal organs and has been validated against a series of six cadaveric experiments on the small female reported by Nahum et al. (1970), Kroell et al. (1974), Viano (1989), Talantikite et al. (1998) and Wilhelm (2003). Results predicted by the model were well-matched to these experimental data for a range of impact speeds and impactor masses. More research is needed in order to increase the accuracy of predicting rib fractures so that the mechanisms responsible for small female injury can be more clearly defined. PMID:17096277

  15. Modeling extreme "Carrington-type" space weather events using three-dimensional global MHD simulations

    NASA Astrophysics Data System (ADS)

    Ngwira, Chigomezyo M.; Pulkkinen, Antti; Kuznetsova, Maria M.; Glocer, Alex

    2014-06-01

    There is a growing concern over possible severe societal consequences related to adverse space weather impacts on man-made technological infrastructure. In the last two decades, significant progress has been made toward the first-principles modeling of space weather events, and three-dimensional (3-D) global magnetohydrodynamics (MHD) models have been at the forefront of this transition, thereby playing a critical role in advancing our understanding of space weather. However, the modeling of extreme space weather events is still a major challenge even for the modern global MHD models. In this study, we introduce a specially adapted University of Michigan 3-D global MHD model for simulating extreme space weather events with a Dst footprint comparable to the Carrington superstorm of September 1859 based on the estimate by Tsurutani et. al. (2003). Results are presented for a simulation run with "very extreme" constructed/idealized solar wind boundary conditions driving the magnetosphere. In particular, we describe the reaction of the magnetosphere-ionosphere system and the associated induced geoelectric field on the ground to such extreme driving conditions. The model setup is further tested using input data for an observed space weather event of Halloween storm October 2003 to verify the MHD model consistence and to draw additional guidance for future work. This extreme space weather MHD model setup is designed specifically for practical application to the modeling of extreme geomagnetically induced electric fields, which can drive large currents in ground-based conductor systems such as power transmission grids. Therefore, our ultimate goal is to explore the level of geoelectric fields that can be induced from an assumed storm of the reported magnitude, i.e., Dst˜=-1600 nT.

  16. Three-dimensional Subsurface Geological Modeling of the Western Osaka Plane based on Borehole Data

    NASA Astrophysics Data System (ADS)

    Nonogaki, S.; Masumoto, S.; Nemoto, T.

    2012-12-01

    Three-dimensional (3D) geological model of subsurface structure plays an important role in developing infrastructures. In particular, the 3D geological model in urban area is quite helpful to solve social problems such as underground utilization, environmental preservation, and disaster assessment. Over the past few years, many studies have been made on algorithms for 3D geological modeling. However, most of them have given little attention to objectivity of the model and traceability of modeling procedures. The purpose of this study is to develop an algorithm for constructing a 3D geological model objectively and for maintaining high-traceability of modeling procedures. For the purpose of our work, we proposed a new algorithm for 3D geological modeling using gridded geological boundary surfaces and the "logical model of geologic structure". The geological boundary surface is given by a form of Digital Elevation Model (DEM). The DEM is generated based on geological information such as elevation, strike and dip by using a unique spline-fitting method. The logical model of geological structure is a mathematical model that defines a positional relation between geological boundary surfaces and geological units. The model is objectively given by recurrence formula derived from a sequence of geological events arranged in chronological order. We applied the proposed algorithm into constructing a 3D subsurface geological model of the western Osaka Plane, southwest Japan. The data used for 3D geological modeling is a set of borehole data provided by Osaka City and Kansai Geoinformatics Agency. As a result, we constructed a 3D model consistent with the subjective model reported in other studies. In addition, all information necessary for modeling, such as the used geological information, the parameters of surface fitting, and the logical model, was stored in text files. In conclusion, we can not only construct 3D geological model objectively but also maintain high

  17. From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets

    PubMed Central

    Murisic, Nebojsa; Hakim, Vincent; Kevrekidis, Ioannis G.; Shvartsman, Stanislav Y.; Audoly, Basile

    2015-01-01

    Epithelial tissue, in which cells adhere tightly to each other and to the underlying substrate, is one of the four major tissue types in adult organisms. In embryos, epithelial sheets serve as versatile substrates during the formation of developing organs. Some aspects of epithelial morphogenesis can be adequately described using vertex models, in which the two-dimensional arrangement of epithelial cells is approximated by a polygonal lattice with an energy that has contributions reflecting the properties of individual cells and their interactions. Previous studies with such models have largely focused on dynamics confined to two spatial dimensions and analyzed them numerically. We show how these models can be extended to account for three-dimensional deformations and studied analytically. Starting from the extended model, we derive a continuum plate description of cell sheets, in which the effective tissue properties, such as bending rigidity, are related explicitly to the parameters of the vertex model. To derive the continuum plate model, we duly take into account a microscopic shift between the two sublattices of the hexagonal network, which has been ignored in previous work. As an application of the continuum model, we analyze tissue buckling by a line tension applied along a circular contour, a simplified set-up relevant to several situations in the developmental contexts. The buckling thresholds predicted by the continuum description are in good agreement with the results of stability calculations based on the vertex model. Our results establish a direct connection between discrete and continuum descriptions of cell sheets and can be used to probe a wide range of morphogenetic processes in epithelial tissues. PMID:26153712

  18. Three-dimensional modeling of Mount Vesuvius with sequential integrated inversion

    NASA Astrophysics Data System (ADS)

    Tondi, Rosaria; de Franco, Roberto

    2003-05-01

    A new image of Mount Vesuvius and the surrounding area is recovered from the tomographic inversion of 693 first P wave arrivals recorded by 314 receivers deployed along five profiles which intersect the crater, and gravity data collected in 17,598 stations on land and offshore. The final three-dimensional (3-D) velocity model presented here is determined by interpolation of five 2-D velocity sections obtained from sequential integrated inversion (SII) of seismic and gravity data. The inversion procedure adopts the "maximum likelihood" scheme in order to jointly optimize seismic velocities and densities. In this way we recover velocity and density models both consistent with seismic and gravity data information. The model parameterization of these 2-D models is chosen in order to keep the diagonal elements of the seismic resolution matrix in the order of 0.2-0.8. The highest values of resolution are detected under the volcano edifice. The imaged 6-km-thick crustal volume underlies a 25 × 45 km2 area. The interpolation is performed by choosing the right grid for a smoothing algorithm which prepares optimum models for asymptotic ray theory methods. Hence this model can be used as a reference model for a 3-D tomographic inversion of seismic data. The 3-D gravity modeling is straightforward. The results of this study clearly image the continuous structure of the Mesozoic carbonate basement top and the connection of the volcano conduit structure to two shallow depressions, which in terms of hazard prevention are the regions through which magma may more easily flow toward the surface and cause possible eruptions.

  19. [Construction and application of economy-pollution-environment three-dimensional evaluation model for district].

    PubMed

    Fan, Xin-Gang; Mi, Wen-Bao; Ma, Zhen-Ning

    2015-02-01

    For deep analysis on the regional environmental economic system, the paper analyzes the mutual relation of regional economy development, environmental quality, environmental pollution, and builds the theoretical basis. Then, the economy-pollution-environment quality three-dimensional coupling evaluation model for district is constructed. It includes economic development level index, environmental pollution index, and environmental quality index. The model is a cube, which has spatialization and visualization characteristics. The model includes 8 sub cubes, which expresses 8 types of state, e. g. low pollution-inferior quality-low level of economic development etc. The model can be used to evaluate the status of region, divide development phase, analyze evolution trend etc. It has two ways including relative meaning evaluation (RME) and absolute meaning evaluation (AME). Based on the model, Yinchuan City in the Ningxia Hui Autonomous Region is used as an example for the empirical study. Using RME, compared with Guangzhou city, The result shows that the Yinchuan City has been a high pollution-low quality-low level of economic development state for a long period during 1996-2010. After 2007, the state changed to a high pollution-high quality