Science.gov

Sample records for accurate three-dimensional models

  1. 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.

  2. Accurate, full-chip, three-dimensional electromagnetic field model for non-Manhattan mask corners

    NASA Astrophysics Data System (ADS)

    Lam, Michael C.; Clifford, Chris; Oliver, Mike; Fryer, David; Tejnil, Edita; Adam, Kostas

    2016-04-01

    The physical process of mask manufacturing produces absorber geometry with significant deviations from the 90-deg corners, which are typically assumed in the mask design. The non-Manhattan mask geometry is an essential contributor to the aerial image and resulting patterning performance through focus. Current state-of-the-art models for corner rounding employ "chopping" a 90-deg mask corner, replacing the corner with a small 45-deg edge. A methodology is presented to approximate the impact of three-dimensional (3-D) EMF effects introduced by corners with rounded edges. The approach is integrated into a full-chip 3-D mask simulation methodology based on the domain decomposition method with edge to edge crosstalk correction.

  3. 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

  4. Accurate landmarking of three-dimensional facial data in the presence of facial expressions and occlusions using a three-dimensional statistical facial feature model.

    PubMed

    Zhao, Xi; Dellandréa, Emmanuel; Chen, Liming; Kakadiaris, Ioannis A

    2011-10-01

    Three-dimensional face landmarking aims at automatically localizing facial landmarks and has a wide range of applications (e.g., face recognition, face tracking, and facial expression analysis). Existing methods assume neutral facial expressions and unoccluded faces. In this paper, we propose a general learning-based framework for reliable landmark localization on 3-D facial data under challenging conditions (i.e., facial expressions and occlusions). Our approach relies on a statistical model, called 3-D statistical facial feature model, which learns both the global variations in configurational relationships between landmarks and the local variations of texture and geometry around each landmark. Based on this model, we further propose an occlusion classifier and a fitting algorithm. Results from experiments on three publicly available 3-D face databases (FRGC, BU-3-DFE, and Bosphorus) demonstrate the effectiveness of our approach, in terms of landmarking accuracy and robustness, in the presence of expressions and occlusions.

  5. 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.

  6. Accurate three-dimensional documentation of distinct sites

    NASA Astrophysics Data System (ADS)

    Singh, Mahesh K.; Dutta, Ashish; Subramanian, Venkatesh K.

    2017-01-01

    One of the most critical aspects of documenting distinct sites is acquiring detailed and accurate range information. Several three-dimensional (3-D) acquisition techniques are available, but each has its own limitations. This paper presents a range data fusion method with the aim to enhance the descriptive contents of the entire 3-D reconstructed model. A kernel function is introduced for supervised classification of the range data using a kernelized support vector machine. The classification method is based on the local saliency features of the acquired range data. The range data acquired from heterogeneous range sensors are transformed into a defined common reference frame. Based on the segmentation criterion, the fusion of range data is performed by integrating finer regions of range data acquired from a laser range scanner with the coarser region of Kinect's range data. After fusion, the Delaunay triangulation algorithm is applied to generate the highly accurate, realistic 3-D model of the scene. Finally, experimental results show the robustness of the proposed approach.

  7. 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.

  8. Bootstrapping the Three Dimensional Supersymmetric Ising Model.

    PubMed

    Bobev, Nikolay; El-Showk, Sheer; Mazáč, Dalimil; Paulos, Miguel F

    2015-07-31

    We implement the conformal bootstrap program for three dimensional conformal field theories with N=2 supersymmetry and find universal constraints on the spectrum of operator dimensions in these theories. By studying the bounds on the dimension of the first scalar appearing in the operator product expansion of a chiral and an antichiral primary, we find a kink at the expected location of the critical three dimensional N=2 Wess-Zumino model, which can be thought of as a supersymmetric analog of the critical Ising model. Focusing on this kink, we determine, to high accuracy, the low-lying spectrum of operator dimensions of the theory, as well as the stress-tensor two-point function. We find that the latter is in an excellent agreement with an exact computation.

  9. 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.

  10. Volumetric techniques: three-dimensional midface modeling

    PubMed Central

    Pierzchała, Ewa; Placek, Waldemar

    2014-01-01

    Aging is a complex process caused by many factors. The most important factors include exposure to UV radiation, smoking, facial muscle movement, gravity, loss and displacement of fat and bone resorption. As a symptom of aging, face loses elasticity, volume and cheerful look. While changing face proportions, the dominant part of a face is its bottom instead of the mid part. The use of three-dimensional face modelling techniques, particularly the mid-face – tear through and cheeks, restores the skin firmness, volume and healthy look. For this purpose the hyaluronic acid is used, calcium hydroxyapatite, and L-polylactic acid fillers. Volumetric techniques require precision and proper selection of the filling agent to give a sense of satisfaction to both the patient and the doctor. PMID:25610354

  11. Volumetric techniques: three-dimensional midface modeling.

    PubMed

    Macierzyńska, Arleta; Pierzchała, Ewa; Placek, Waldemar

    2014-12-01

    Aging is a complex process caused by many factors. The most important factors include exposure to UV radiation, smoking, facial muscle movement, gravity, loss and displacement of fat and bone resorption. As a symptom of aging, face loses elasticity, volume and cheerful look. While changing face proportions, the dominant part of a face is its bottom instead of the mid part. The use of three-dimensional face modelling techniques, particularly the mid-face - tear through and cheeks, restores the skin firmness, volume and healthy look. For this purpose the hyaluronic acid is used, calcium hydroxyapatite, and L-polylactic acid fillers. Volumetric techniques require precision and proper selection of the filling agent to give a sense of satisfaction to both the patient and the doctor.

  12. 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.

  13. Three-dimensional modelling of Venus photochemistry

    NASA Astrophysics Data System (ADS)

    Stolzenbach, Aurélien; Lefèvre, Franck; Lebonnois, Sébastien; Määttänen, Anni; Bekki, Slimane

    2014-05-01

    We have developed a new code of the Venus atmospheric chemistry based on our photochemical model already in use for Mars (e.g., Lefèvre et al., J. Geophys. Res., 2004). For Venus, the code also includes a parameterized treatment of cloud microphysics that computes the composition of sulphuric acid droplets and their number density based on a given droplet size distribution in altitude. We coupled this photochemical-microphysical package to the LMD general circulation model of Venus (Lebonnois et al., J. Geophys. Res., 2010) with a sedimentation module recently added. We will describe preliminary results obtained with this first three-dimensional model of the Venus photochemistry. The space and time distribution of key chemical species as well as the modelled clouds characteristics will be detailed and compared to observations performed from Venus Express and from the Earth (e.g. Knollenberg and Hunten, J. Geophys. Res., 1980 ; Wilquet et al., J. Geophys. Res., 2009 ; Sandor et al., Icarus, 2012).

  14. Three-Dimensional Modelling of Venus Photochemistry

    NASA Astrophysics Data System (ADS)

    Stolzenbach, A.; Lefèvre, F.; Lebonnois, S.; Maattanen, A. E.; Bekki, S.

    2015-12-01

    We have developed a new code of the Venus atmospheric chemistry based on our photochemical model already in use for Mars (e.g., Lefèvre et al., J. Geophys. Res., 2004). For Venus, the code also includes a parameterized treatment of cloud microphysics that computes the composition of sulphuric acid droplets and their number density based on a given droplet size distribution in altitude and latitude. We coupled this photochemical-microphysical package to the LMD general circulation model of Venus (Lebonnois et al., J. Geophys. Res., 2010) with a sedimentation module that takes into account the parametrized droplet size distribution. We will describe the results obtained with this first three-dimensional model of the Venus photochemistry. The space and time distribution of key chemical species as well as the modelled clouds characteristics will be detailed and compared to observations performed from Venus Express and from the Earth (e.g. Knollenberg and Hunten, J. Geophys. Res., 1980 ; Wilquet et al., J. Geophys. Res., 2009 ; Sandor et al., Icarus, 2012 ; Mahieux et al., PSS, 2014 ; Marcq et al., 2015, PSS).

  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 visualization for large models

    NASA Astrophysics Data System (ADS)

    Roth, Michael W.

    2001-09-01

    High-resolution (0.3-1 m) digital-elevation data is widely available from commercial sources. Whereas the production of two-dimensional (2D) mapping products from such data is standard practice, the visualization of such three-dimensional (3D) data has been problematic. The basis for this problem is the same as that for the large-model problem in computer graphics-- large amounts of geometry are difficult for current rendering algorithms and hardware. This paper describes a cost-effective solution to this problem that has two parts. First is the employment of the latest in cost-effective 3D chips and video boards that have recently emerged. The second part is the employment of quad-tree data structures for efficient data storage and retrieval during rendering. The result is the capability for real-time display of large (over tens of millions of samples) digital elevation models on modest PC-based systems. This paper shows several demonstrations of this approach using airborne lidar data. The implication of this work is a paradigm shift for geo-spatial information systems--3D data can now be as easy to use as 2D data.

  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. 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.

  20. 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.

  1. Three-dimensional chemotaxis model for a crawling neutrophil.

    PubMed

    Song, Jihwan; Kim, Dongchoul

    2010-11-01

    Chemotactic cell migration is a fundamental phenomenon in complex biological processes. A rigorous understanding of the chemotactic mechanism of crawling cells has important implications for various medical and biological applications. In this paper, we propose a three-dimensional model of a single crawling cell to study its chemotaxis. A single-cell study of chemotaxis has an advantage over studies of a population of cells in that it provides a clearer observation of cell migration, which leads to more accurate assessments of chemotaxis. The model incorporates the surface energy of the cell and the interfacial interaction between the cell and substrate. The semi-implicit Fourier spectral method is applied to achieve high efficiency and numerical stability. The simulation results provide the kinetic and morphological traits of a crawling cell during chemotaxis.

  2. Numerical Modeling of Three-Dimensional Confined Flows

    NASA Technical Reports Server (NTRS)

    Greywall, M. S.

    1981-01-01

    A three dimensional confined flow model is presented. The flow field is computed by calculating velocity and enthalpy along a set of streamlines. The finite difference equations are obtained by applying conservation principles to streamtubes constructed around the chosen streamlines. With appropriate substitutions for the body force terms, the approach computes three dimensional magnetohydrodynamic channel flows. A listing of a computer code, based on this approach is presented in FORTRAN IV language. The code computes three dimensional compressible viscous flow through a rectangular duct, with the duct cross section specified along the axis.

  3. Three-dimensional laser radar modeling

    NASA Astrophysics Data System (ADS)

    Steinvall, Ove K.; Carlsson, Tomas

    2001-09-01

    Laser radars have the unique capability to give intensity and full 3-D images of an object. Doppler lidars can give velocity and vibration characteristics of an objects. These systems have many civilian and military applications such as terrain modelling, depth sounding, object detection and classification as well as object positioning. In order to derive the signal waveform from the object one has to account for the laser pulse time characteristics, media effects such as the atmospheric attenuation and turbulence effects or scattering properties, the target shape and reflection (BRDF), speckle noise together with the receiver and background noise. Finally the type of waveform processing (peak detection, leading edge etc.) is needed to model the sensor output to be compared with observations. We have developed a computer model which models performance of a 3-D laser radar. We will give examples of signal waveforms generated from model different targets calculated by integrating the laser beam profile in space and time over the target including reflection characteristics during different speckle and turbulence conditions. The result will be of help when designing and using new laser radar systems. The importance of different type of signal processing of the waveform in order to fulfil performance goals will be shown.

  4. Applications of three-dimensionally scanned models in orthodontics.

    PubMed

    Cha, B K; Choi, J I; Jost-Brinkmann, P G; Jeong, Y M

    2007-01-01

    The purpose of this study was to investigate clinical applications of the three-dimensional reverse engineering technologies for the analysis of orthodontic models. The measuring accuracy and the process of the 3D model scanning technique were evaluated with respect to linear, surface and volumetric parameters. Orthodontically induced dentoalveolar changes, which have been traditionally evaluated by cephalometric analysis, were assessed by the registration function of Rapidform 2002, a 3D-reverse modeling software in scanned maxillary casts. Three-dimensional digital models are valuable alternatives to conventional casts for model analysis and also yield information which could previously be gathered only by cephalometric superimposition.

  5. Shape memory polymers: three-dimensional isotropic modeling

    NASA Astrophysics Data System (ADS)

    Balogun, Olaniyi; Mo, Changki

    2014-04-01

    This paper presents a comprehensive three-dimensional isotropic numerical simulation for a thermo-mechanical constitutive model of shape memory polymers (SMPs). In order to predict the thermo-mechanical behavior of SMPs, a one-dimensional rheological thermo-mechanical constitutive model is adopted, translated into a three-dimensional form and a time discrete form of the three-dimensional model is then presented. Numerical simulation of this model was developed using the UMAT subroutine capabilities of the finite element software ABAQUS. Evolution of the analysis was conducted by making use of the backward difference scheme, which was applied to all quantities within the model, including the material properties. A comparison of the numerical simulation results was carried out with the available experimental data. Numerical simulation results clearly exhibit the thermo-mechanical properties of the material which include shape fixity, shape recovery, and recovery stress. Finally, a prediction for the transverse and shear directions of the material is presented.

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

    PubMed

    Nakayama, Yu

    2016-04-08

    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. 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)

  8. 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...

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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.

  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 Modeling of Air-Sea Interaction

    NASA Astrophysics Data System (ADS)

    Regis, J. L.; Slinn, D. N.

    2004-12-01

    Deep-water wave breaking is crucial in the transfer of heat, gases, and momentum between the ocean and the atmosphere. Observations of these events have provided qualitative support to this end, and yet accurate quantification of momentum transfer for strong winds and nonlinear waves has remained a challenge. In recent years, advances have been made in the development of numerous algorithms to capture and describe air-sea interaction. Most, however, are idealized and only capable of modeling fluid flow within the two-dimensional approximation. Thus, many important characteristics of the flow composition and breaking process are ignored, oversimplified, or remain unknown. We employ a three-dimensional, time-dependent, finite difference, volume of fluid model, including both the flow of air and water, entitled TRUCHAS, to address the issue of deep-water breaking waves. Our model utilizes the multidimensional piecewise linear interface calculation method to assess the volume fraction of each fluid material in every mesh cell. The model solves conservation equations for mass and momentum for multiple fluids within the domain and tracks the interfaces between them. A great many details of the flow development are available for analysis from the model output. These include wind and water velocities, pressure gradients in both the air and sea around a breaking wave, the development and evolution of wind-generated waves, and the corresponding transfer of momentum from the atmosphere to the ocean. Our results are correlated with laboratory experiments conducted at the University of Miami's Air-Sea Interaction Salt-water Tank that possesses both wind and wave generating capabilities. Preliminary model results show good qualitative agreement to laboratory data.

  13. 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.

  14. 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.

  15. Three dimensional thermobaric modeling of a gas hydrate system

    NASA Astrophysics Data System (ADS)

    Williams, Amanda Quigley

    Seismic imaging is recognized as the most cost effective method for identifying the presence of gas hydrate resources. The base of the gas hydrate stability zone is recognized by the presence of regionally extensive bottom simulating reflectors (BSR). However, in some areas such as the Gulf of Mexico, regionally extensive BSRs are not found. In such cases, an understanding of the thermobaric conditions may be used to determine the location of gas hydrates and the base of the gas hydrate stability zone. The aim of this research is to combine seismic velocity analysis and thermal modeling to predict the base of the hydrate stability zone. As a case study, we apply this modeling to the extensively documented site at Woolsey Mound, MC-118, Gulf of Mexico. Woolsey Mound, and much of the Gulf of Mexico, has been greatly affected by salt tectonics. Multiple seismic and CHIRP surveys have been collected at Woolsey Mound, but the base of the gas hydrate stability zone has been elusive due to the complexities associated with the presence of salt. The velocity analysis and previous studies on the sedimentary environment were the basis to derive the thermal and salinity conditions. Data from the heat flow survey provide an upper boundary condition at the sea floor in order to create a more accurate thermal model; the velocity model helped accurately place the salt diapir within the mound system. Hydrate phase equilibrium models were used to estimate a thermobaric model for Woolsey Mound. Using two different salinity gradients, the base of the gas hydrate stability zone was found to be located within 70 m of the seafloor with a salt concentration up to 90% at the shallowest point of the salt diapir, and 120 m of the seafloor with a salt concentration up to standard temperature and pressure conditions of salt (of approximately 56%) at the shallowest point of the salt diapir. This study provides a preliminary look at how the temperature and salinity affect the depth at which gas

  16. Three-dimensional modeling of the human fallopian tube fimbriae

    PubMed Central

    Eddie, Sharon L.; Quartuccio, Suzanne M.; Zhu, Jie; Shepherd, Jessica A.; Kothari, Rajul; Kim, J. Julie; Woodruff, Teresa K.; Burdette, Joanna E.

    2015-01-01

    Objective Ovarian cancer is the most lethal gynecological malignancy that affects women. Recent data suggests the disease may originate in the fallopian fimbriae; however, the anatomical origin of ovarian carcinogenesis remains unclear. This is largely driven by our lack of knowledge regarding the structure and function of normal fimbriae and the relative paucity of models that accurately recapitulate the in vivo fallopian tube. Therefore, a human three-dimensional (3D) culture system was developed to examine the role of the fallopian fimbriae in serous tumorigenesis. Methods Alginate matrix was utilized to support human fallopian fimbriae ex vivo. Fimbriae were cultured with factors hypothesized to contribute to carcinogenesis, namely; H2O2 (1mM) a mimetic of oxidative stress, insulin (5 µg/ml) to stimulate glycolysis, and estradiol (E2, 10nM) which peaks before ovulation. Cultures were evaluated for changes in proliferation and p53 expression, criteria utilized to identify potential precursor lesions. Further, secretory factors were assessed after treatment with E2 to identify if steroid signaling induces a pro-tumorigenic microenvironment. Results 3D fimbriae cultures maintained normal tissue architecture up to 7 days, retaining both epithelial subtypes. Treatment of cultures with H2O2 or insulin significantly induced proliferation. However, p53 stabilization was unaffected by any particular treatment, although was induced by ex vivo culturing. Moreover, E2-alone treatment significantly induced its canonical target PR and expression of IL8, a factor linked to poor outcome. Conclusions 3D alginate cultures of human fallopian fimbriae provide an important microphysicological model, which can be further utilized to investigate serous tumorigenesis originating from the fallopian tube. PMID:25527363

  17. 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.

  18. Modeling Cometary Coma with a Three Dimensional, Anisotropic Multiple Scattering Distributed Processing Code

    NASA Technical Reports Server (NTRS)

    Luchini, Chris B.

    1997-01-01

    Development of camera and instrument simulations for space exploration requires the development of scientifically accurate models of the objects to be studied. Several planned cometary missions have prompted the development of a three dimensional, multi-spectral, anisotropic multiple scattering model of cometary coma.

  19. A Three Dimensional Non-Singular Modelling of Rigid Manipulators.

    DTIC Science & Technology

    1987-12-01

    511111 OTC FILE COPY (1) ’ NAVAL POSTGRADUATE SCHOOL 0 ’ Monterey, California IDTIC I{ IELECTE S MAR 08 8 f 0? THESIS A THREE DIMENSIONAL NON-SINGULAR...MODELLING OF RIGID MANIPULATORS by Sadrettin Altinok December 1987 Thesis Advisor D.L. Smith Approved for public release; distribution is unlimited. 88...MASTERS THESIS FROM _ TO 1987 DECEMBER iC 6 16 SUPPLEMENTARY NOTATION 17 COSA T i CODES 18 SUBJECT TERMS (Continue on reverse f necessary and identify by

  20. 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.

  1. 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.

  2. Fiddler crabs accurately measure two-dimensional distance over three-dimensional terrain.

    PubMed

    Walls, Michael L; Layne, John E

    2009-10-01

    Foraging fiddler crabs (Uca spp.) monitor the location of, and are able to return to, their burrows by employing path integration. This requires them to accurately measure both the directions and distances of their locomotory movements. Even though most fiddler crabs inhabit relatively flat terrain, they must cope with vertical features of their environment, such as sloping beaches, mounds and shells, which may represent significant obstacles. To determine whether fiddler crabs can successfully perform path integration among such three-dimensional obstacles, we tested their ability to measure distance while we imposed a vertical detour. By inserting a large hill in the homeward path of foraging crabs we show that fiddler crabs can cope with vertical detours: they accurately travel the correct horizontal distance, despite the fact that the shape of the hill forces them to change their gait from what would be used on flat ground. Our results demonstrate a flexible path integrator capable of measuring, and either integrating or discarding, the vertical dimension.

  3. Numerical solutions of the three-dimensional magnetohydrodynamic alpha model.

    PubMed

    Mininni, Pablo D; Montgomery, David C; Pouquet, Annick

    2005-04-01

    We present direct numerical simulations and alpha -model simulations of four familiar three-dimensional magnetohydrodynamic (MHD) turbulence effects: selective decay, dynamic alignment, inverse cascade of magnetic helicity, and the helical dynamo effect. The MHD alpha model is shown to capture the long-wavelength spectra in all these problems, allowing for a significant reduction of computer time and memory at the same kinetic and magnetic Reynolds numbers. In the helical dynamo, not only does the alpha model correctly reproduce the growth rate of magnetic energy during the kinematic regime, it also captures the nonlinear saturation level and the late generation of a large scale magnetic field by the helical turbulence.

  4. A Three-dimensional Topological Model of Ternary Phase Diagram

    NASA Astrophysics Data System (ADS)

    Mu, Yingxue; Bao, Hong

    2017-01-01

    In order to obtain a visualization of the complex internal structure of ternary phase diagram, the paper realized a three-dimensional topology model of ternary phase diagram with the designed data structure and improved algorithm, under the guidance of relevant theories of computer graphics. The purpose of the model is mainly to analyze the relationship between each phase region of a ternary phase diagram. The model not only obtain isothermal section graph at any temperature, but also extract a particular phase region in which users are interested.

  5. Three-dimensional modeling of propagating precipitation waves.

    PubMed

    Tinsley, Mark R; Collison, Darrell; Showalter, Kenneth

    2015-06-01

    A general three-dimensional model for propagating precipitation waves is presented. Structural features identified in experimental studies of propagating waves in the AlCl3/NaOH and NaAl(OH)4/HCl systems are described by the 3D model. Two forms of precipitate with different physical properties play key mechanistic roles in the wave propagation. Experimentally observed circular and spiral waves are simulated by the 3D model, as well as wave annihilation on the collision of two waves.

  6. 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.

  7. Modelling Three-Dimensional Sound Propagation in Wedge Environments

    NASA Astrophysics Data System (ADS)

    Austin, Melanie Elizabeth

    Ocean environments with sloped seafloors can give rise to sound paths that do not remain in a constant plane of propagation. Numerical modelling of sound fields in such environments requires the use of computer models that fully account for out-of-plane sound propagation effects. The inclusion of these three-dimensional effects can be computationally intensive and the effects are often neglected in computer sound propagation codes. The current state-of-the art in sound propagation modelling has seen the development of models that can fully account for out-of-plane sound propagation. Such a model has been implemented in this research to provide acoustic consultants JASCO Applied Sciences with an important tool for environmental noise impact assessment in complicated marine environments. The model is described and validation results are shown for benchmark test cases. The model is also applied to study three-dimensional propagation effects in measured data from a realistic ocean environment. Particular analysis techniques assist in the interpretation of the modelled sound field for this physical test environment providing new insight into the characteristics of the test environment.

  8. Three-dimensional nanojunction device models for photovoltaics

    NASA Astrophysics Data System (ADS)

    Wangperawong, Artit; Bent, Stacey F.

    2011-06-01

    A model is developed to describe the behavior of three-dimensionally nanostructured photovoltaic devices, distinguishing between isolated radial pn junctions and interdigitated pn junctions. We examine two specific interdigitated architectures, the point-contact nanojunction and the extended nanojunction, which are most relevant to experimental devices reported to date but have yet to be distinguished in the field. The model is also applied to polycrystalline CdTe devices with inverted grain boundaries. We demonstrate that for CdTe/CdS solar cells using low-quality materials, the efficiency of the extended nanojunction geometry is superior to other designs considered.

  9. 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.

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

    PubMed

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

    2015-10-07

    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.

  11. 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

  12. Three Dimensional Visualization of a Coastal Mesoscale Model

    DTIC Science & Technology

    1993-12-01

    thankful to Karen, my wife, who managed to keep the faith as well as grow a beautiful daughter, Danielle Tayler Sampson -- our first. Danielle, I ...No I I TITLE (include secutray class•ncarronii Three Dimensional Visualization of a Coastal Mesoscale Model 12 PERSONAl. AUTHOR(S) Sampson, R. Mark 1...3a TYPE OF REPORT 13b TIME COVERED 114 DATE OF REPORT (year, monA daiv; I PAGE COUN.NT Master’s Thesis Fr To 93 December 70 16 SUPPLEMENTARY NOTATION

  13. Assessment of higher order turbulence models for complex two- and three-dimensional flowfields

    NASA Technical Reports Server (NTRS)

    Menter, Florian R.

    1992-01-01

    A numerical method is presented to solve the three-dimensional Navier-Stokes equations in combination with a full Reynolds-stress turbulence model. Computations will be shown for three complex flowfields. The results of the Reynolds-stress model will be compared with those predicted by two different versions of the k-omega model. It will be shown that an improved version of the k-omega model gives as accurate results as the Reynolds-stress model.

  14. Assessing Predicted Contacts for Building Protein Three-Dimensional Models.

    PubMed

    Adhikari, Badri; Bhattacharya, Debswapna; Cao, Renzhi; Cheng, Jianlin

    2017-01-01

    Recent successes of contact-guided protein structure prediction methods have revived interest in solving the long-standing problem of ab initio protein structure prediction. With homology modeling failing for many protein sequences that do not have templates, contact-guided structure prediction has shown promise, and consequently, contact prediction has gained a lot of interest recently. Although a few dozen contact prediction tools are already currently available as web servers and downloadables, not enough research has been done towards using existing measures like precision and recall to evaluate these contacts with the goal of building three-dimensional models. Moreover, when we do not have a native structure for a set of predicted contacts, the only analysis we can perform is a simple contact map visualization of the predicted contacts. A wider and more rigorous assessment of the predicted contacts is needed, in order to build tertiary structure models. This chapter discusses instructions and protocols for using tools and applying techniques in order to assess predicted contacts for building three-dimensional models.

  15. Three-dimensional cell culture models for investigating human viruses.

    PubMed

    He, Bing; Chen, Guomin; Zeng, Yi

    2016-10-01

    Three-dimensional (3D) culture models are physiologically relevant, as they provide reproducible results, experimental flexibility and can be adapted for high-throughput experiments. Moreover, these models bridge the gap between traditional two-dimensional (2D) monolayer cultures and animal models. 3D culture systems have significantly advanced basic cell science and tissue engineering, especially in the fields of cell biology and physiology, stem cell research, regenerative medicine, cancer research, drug discovery, and gene and protein expression studies. In addition, 3D models can provide unique insight into bacteriology, virology, parasitology and host-pathogen interactions. This review summarizes and analyzes recent progress in human virological research with 3D cell culture models. We discuss viral growth, replication, proliferation, infection, virus-host interactions and antiviral drugs in 3D culture models.

  16. Digital vision system for three-dimensional model acquisition

    NASA Astrophysics Data System (ADS)

    Yuan, Ta; Lin, Huei-Yung; Qin, Xiangdong; Subbarao, Murali

    2000-10-01

    A digital vision system and the computational algorithms used by the system for three-dimensional (3D) model acquisition are described. The system is named Stonybrook VIsion System (SVIS). The system can acquire the 3D model (which includes the 3D shape and the corresponding image texture) of a simple object within a 300 mm X 300 mm X 300 mm volume placed about 600 mm from the system. SVIS integrates Image Focus Analysis (IFA) and Stereo Image Analysis (SIA) techniques for 3D shape and image texture recovery. First, 4 to 8 partial 3D models of the object are obtained from 4 to 8 views of the object. The partial models are then integrated to obtain a complete model of the object. The complete model is displayed using a 3D graphics rendering software (Apple's QuickDraw). Experimental results on several objects are presented.

  17. An introduction to three-dimensional climate modeling

    NASA Technical Reports Server (NTRS)

    Washington, W. M.; Parkinson, C. L.

    1986-01-01

    The development and use of three-dimensional computer models of the earth's climate are discussed. The processes and interactions of the atmosphere, oceans, and sea ice are examined. The basic theory of climate simulation which includes the fundamental equations, models, and numerical techniques for simulating the atmosphere, oceans, and sea ice is described. Simulated wind, temperature, precipitation, ocean current, and sea ice distribution data are presented and compared to observational data. The responses of the climate to various environmental changes, such as variations in solar output or increases in atmospheric carbon dioxide, are modeled. Future developments in climate modeling are considered. Information is also provided on the derivation of the energy equation, the finite difference barotropic forecast model, the spectral transform technique, and the finite difference shallow water waved equation model.

  18. 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.

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

    PubMed Central

    Liu, Taoming; Çavuşoğlu, 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

  20. Automated photogrammetry for three-dimensional models of urban spaces

    NASA Astrophysics Data System (ADS)

    Leberl, Franz; Meixner, Philipp; Wendel, Andreas; Irschara, Arnold

    2012-02-01

    The location-aware Internet is inspiring intensive work addressing the automated assembly of three-dimensional models of urban spaces with their buildings, circulation spaces, vegetation, signs, even their above-ground and underground utility lines. Two-dimensional geographic information systems (GISs) and municipal utility information exist and can serve to guide the creation of models being built with aerial, sometimes satellite imagery, streetside images, indoor imaging, and alternatively with light detection and ranging systems (LiDARs) carried on airplanes, cars, or mounted on tripods. We review the results of current research to automate the information extraction from sensor data. We show that aerial photography at ground sampling distances (GSD) of 1 to 10 cm is well suited to provide geometry data about building facades and roofs, that streetside imagery at 0.5 to 2 cm is particularly interesting when it is collected within community photo collections (CPCs) by the general public, and that the transition to digital imaging has opened the no-cost option of highly overlapping images in support of a more complete and thus more economical automation. LiDAR-systems are a widely used source of three-dimensional data, but they deliver information not really superior to digital photography.

  1. 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.

  2. 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.

  3. A three dimensional heart model based on anatomically aligned trusses.

    PubMed

    Witman, S; Gefen, A; Barnea, O

    2007-01-01

    A new approach for modeling and simulating the contraction of the heart is presented. The model is based on anatomical images and accounts for cardiac muscle fibers and their orientation. The heart is modeled as a structure built of trusses, each representing a group of myofibers with calculated deformations using matrix structural analysis. Three elements are represented; these are the contractile cardiac muscle, the elastic passive collagen, and intracardiac blood interacting with the heart's preload and afterload. Incompressibility of each element is preserved. The conduction system is simulated in the model by transferring the activating signal from one element to another or by Purkinje fibers activation. The method was demonstrated using a three-dimensional one-layer geometrical ventricle with orthogonal fibers and with anatomically oriented fibers.

  4. Recursive three-dimensional model reconstruction based on Kalman filtering.

    PubMed

    Yu, Ying Kin; Wong, Kin Hong; Chang, Michael Ming Yuen

    2005-06-01

    A recursive two-step method to recover structure and motion from image sequences based on Kalman filtering is described in this paper. The algorithm consists of two major steps. The first step is an extended Kalman filter (EKF) for the estimation of the object's pose. The second step is a set of EKFs, one for each model point, for the refinement of the positions of the model features in the three-dimensional (3-D) space. These two steps alternate from frame to frame. The initial model converges to the final structure as the image sequence is scanned sequentially. The performance of the algorithm is demonstrated with both synthetic data and real-world objects. Analytical and empirical comparisons are made among our approach, the interleaved bundle adjustment method, and the Kalman filtering-based recursive algorithm by Azarbayejani and Pentland. Our approach outperformed the other two algorithms in terms of computation speed without loss in the quality of model reconstruction.

  5. 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.

  6. Three-dimensional percolation modeling of self-healing composites.

    PubMed

    Dementsov, Alexander; Privman, Vladimir

    2008-08-01

    We study the self-healing process of materials with embedded "glue"-carrying cells, in the regime of the onset of the initial fatigue. Three-dimensional numerical simulations within the percolation-model approach are reported. The main numerical challenge taken up in the present work has been to extend the calculation of the conductance to three-dimensional lattices. Our results confirm the general features of the process: The onset of material fatigue is delayed, by development of a plateaulike time dependence of the material quality. We demonstrate that, in this low-damage regime, the changes in the conductance and thus in similar transport and response properties of the material can be used as measures of the material quality degradation. A new feature found for three dimensions, where it is much more profound than in earlier-studied two-dimensional systems, is the competition between the healing cells. Even for low initial densities of the healing cells, they interfere with each other and reduce each other's effective healing efficiency.

  7. Emerging role of three-dimensional speckle tracking strain for accurate quantification of left ventricular dyssynchrony.

    PubMed

    Tanaka, Hidekazu; Tatsumi, Kazuhiro; Matsumoto, Kensuke; Kawai, Hiroya; Hirata, Ken-ichi

    2013-10-01

    A case was 53-year-old female with dilated-phase hypertrophic cardiomyopathy. She was classified as New York Heart Association functional class III heart failure despite receiving optimal medical therapy. The electrocardiogram taken showed intraventricular conduction delay with a QRS width of 194 msec. The left ventricular (LV) end-diastolic and systolic volumes, and ejection fraction (EF) were 101 mL, 68 mL, and 32%, respectively. The patient showed no significant mechanical LV dyssynchrony as evidenced by two-dimensional (2D) speckle tracking radial strain, which is defined as the time difference between anterior-septum and posterior wall, of 105 msec (<130 msec). Three-dimensional (3D) speckle tracking radial strain was performed for more detailed LV mechanical dyssynchrony analysis. An especially important finding for 3D speckle tracking radial strain analysis was that the average time-to-peak strain of 5 septum segments at 3 different LV levels (basal-anterior-septum, basal-septum, mid-anterior-septum, mid-septum, apical-septum) was significantly shorter than that of 5 posterolateral segments at 3 different LV levels (basal-posterior, basal-lateral, mid-posterior, mid-lateral, apical-lateral). This time difference between septum and posterolateral wall was 216 msec (204 msec vs. 420 msec), which was considered to indicate significant LV mechanical dyssynchrony (≥130 msec). 12 months after cardiac resynchronization therapy (CRT), EF had improved to 47%, while end-systolic and diastolic volumes had decreased to 88 mL and 47 mL, respectively, so that the patient was classified as a responder. In conclusions, a newly developed 3D speckle tracking strain can provide a comprehensive evaluation of "true" LV mechanical dyssynchrony from pyramidal 3D data sets acquired in the same beat, thus yielding more accurate information than previously possible with the 2D speckle tracking system.

  8. 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.

  9. 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.

  10. 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.

  11. Three-dimensional vertex model for simulating multicellular morphogenesis

    PubMed Central

    Okuda, Satoru; Inoue, Yasuhiro; Adachi, Taiji

    2015-01-01

    During morphogenesis, various cellular activities are spatiotemporally coordinated on the protein regulatory background to construct the complicated, three-dimensional (3D) structures of organs. Computational simulations using 3D vertex models have been the focus of efforts to approach the mechanisms underlying 3D multicellular constructions, such as dynamics of the 3D monolayer or multilayer cell sheet like epithelia as well as the 3D compacted cell aggregate, including dynamic changes in layer structures. 3D vertex models enable the quantitative simulation of multicellular morphogenesis on the basis of single-cell mechanics, with complete control of various cellular activities such as cell contraction, growth, rearrangement, division, and death. This review describes the general use of the 3D vertex model, along with its applications to several simplified problems of developmental phenomena. PMID:27493850

  12. 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.

  13. 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.

  14. Downhole-electrode resistivity interpretation with three-dimensional models

    SciTech Connect

    Newkirk, D.J.

    1982-06-01

    Using an integral equation numerical solution, the theoretical results for (1) the potential, (2) the apparent resistivity calculated from the total horizontal electric field, (3) the apparent resistivity calculated from the potential due to different three-dimensional bodies in plan and cross-section views have been computed. The transmitter consists of a remote electrode and a dowhole electrode embedded in the body or located near the body. For hole-to-surface work, the potential offers little information about the parameters of a deep body. The apparent resistivity from the total electric field, with its distinctive patterns, best resolves the width, length, and dip of the model, while the apparent resistivity from the potential is more difficult to interpret. The cross-section views, for analysis of hole-to-hole surveys, theoretically define the body for the potential and the apparent resistivity derived from the potential, but their use in practice is limited.

  15. 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.

  16. 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.

  17. Digital Moon: A three-dimensional framework for lunar modeling

    NASA Astrophysics Data System (ADS)

    Paige, D. A.; Elphic, R. C.; Foote, E. J.; Meeker, S. R.; Siegler, M. A.; Vasavada, A. R.

    2009-12-01

    The Moon has a complex three-dimensional shape with significant large-scale and small-scale topographic relief. The Moon’s topography largely controls the distribution of incident solar radiation, as well as the scattered solar and infrared radiation fields. Topography also affects the Moon’s interaction with the space environment, its magnetic field, and the propagation of seismic waves. As more extensive and detailed lunar datasets become available, there is an increasing need to interpret and compare them with the results of physical models in a fully three-dimensional context. We have developed a three-dimensional framework for lunar modeling we call the Digital Moon. The goal of this work is to enable high fidelity physical modeling and visualization of the Moon in a parallel computing environment. The surface of the Moon is described by a continuous triangular mesh of arbitrary shape and spatial scale. For regions of limited geographic extent, it is convenient to employ meshes on a rectilinear grid. However for global-scale modeling, we employ a continuous geodesic gridding scheme (Teanby, 2008). Each element in the mesh surface is allowed to have a unique set of physical properties. Photon and particle interactions between mesh elements are modeled using efficient ray tracing algorithms. Heat, mass, photon and particle transfer within each mesh element are modeled in one dimension. Each compute node is assigned a portion of the mesh and collective interactions between elements are handled through network interfaces. We have used the model to calculate lunar surface and subsurface temperatures that can be compared directly with radiometric temperatures measured by the Diviner Lunar Radiometer Experiment on the Lunar Reconnaissance Orbiter. The model includes realistic surface photometric functions based on goniometric measurements of lunar soil samples (Foote and Paige, 2009), and one-dimensional thermal models based on lunar remote sensing and Apollo

  18. 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.

  19. A Three-dimensional Babcock-Leighton Solar Dynamo Model

    NASA Astrophysics Data System (ADS)

    Miesch, Mark S.; Dikpati, Mausumi

    2014-04-01

    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.

  20. 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.

  1. Three-dimensional effects for radio frequency antenna modeling

    SciTech Connect

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

    1994-10-15

    Electromagnetic field calculations for radio frequency (rf) antennas in two dimensions (2-D) neglect finite antenna length effects as well as the feeders leading to the main current strap. The 2-D calculations predict that the return currents in the sidewalls of the antenna structure depend strongly on the plasma parameters, but this prediction is suspect because of experimental evidence. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform three-dimensional (3-D) modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused 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.

  2. 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.

  3. Three-dimensional model for subsurface transport and biodegradation

    SciTech Connect

    Waddill, D.W.; Widdowson, M.A.

    1998-04-01

    This paper describes and demonstrates a numerical model for subsurface solute transport with aerobic and sequential anaerobic biodegradation. The model can depict multiple constituents in a three-dimensional (3D), anisotropic, heterogeneous domain. Hydrocarbon contaminants are simulated as electron donors for microbial growth, and available electron acceptors (EAs) may be utilized simultaneously or in the following sequence: O{sub 2}, NO{sub 3}{sup {minus}}, Mn(IV), Fe(III), SO{sub 4}{sup 2{minus}}, and CO{sub 2}. The model can account for Mn(II), Fe(II), H{sub w}S, CH{sub 4}, and a user-defined nitrogenous compound as products of biodegradation. Biodegradation of each hydrocarbon substrate follows Monod kinetics, modified to include the effects of EA and nutrient availability. Inhibition functions allow any EA to inhibit the utilization of all other EAs that provide less energy to the microbes. Microbial biomass is conceptualized as scattered microcolonies attached to the porous medium. The model assumes that interphase diffusion limitations to microbial growth are negligible and no geometrical parameters are assigned to the colonies. The behavior of the model was demonstrated using simple, hypothetical test cases. Transport of a biodegradable hydrocarbon was compared to a nonbiodegradable tracer in a 3D, hypothetical domain. Anaerobic biodecay significantly reduced predicted contaminant concentrations and travel distance. Biodegradation of the total contaminant mass depends on EA availability and did not follow first-order kinetics.

  4. A three-dimensional computational model of collagen network mechanics.

    PubMed

    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.

  5. A Three-dimensional Model of Tangential YORP

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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.

  6. 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.

  7. Up and down cascades: three-dimensional magnetic field model.

    PubMed

    Blanter, E M; Shnirman, M G; Le Mouël, J L

    2002-06-01

    In our previous works we already have proposed a two-dimensional model of geodynamo. Now we use the same approach to build a three-dimensional self-excited geodynamo model that generates a large scale magnetic field from whatever small initial field, using the up and down cascade effects of a multiscale turbulent system of cyclones. The multiscale system of turbulent cyclones evolves in six domains of an equatorial cylindrical layer of the core. The appearance of new cyclones is realized by two cascades: a turbulent direct cascade and an inverse cascade of coupling of similar cyclones. The interaction between the different domains is effected through a direct cascade parameter which is essential for the statistics of the long-life symmetry breaking. Generation of the secondary magnetic field results from the interaction of the components of the primary magnetic field with the turbulent cyclones. The amplification of the magnetic field is due to the transfer of energy from the turbulent helical motion to the generated magnetic field. The model demonstrates a phase transition through the parameter characterizing this energy transfer. In the supercritical domain we obtain long-term intervals of constant polarity (chrons) and quick reversals; relevant time constants agree with paleomagnetic observations. Possible application of the model to the study of the geometrical structure of the geomagnetic field (and briefly other planetary fields) is discussed.

  8. Three-dimensional modeling of hearing in Delphinus delphis.

    PubMed

    Aroyan, J L

    2001-12-01

    Physical modeling is a fertile approach to investigating sound emission and reception (hearing) in marine mammals. A method for simulation of hearing was developed combining three-dimensional acoustic propagation and extrapolation techniques with a novel approach to modeling the acoustic parameters of mammalian tissues. Models of the forehead and lower jaw tissues of the common dolphin, Delphinus delphis, were created in order to simulate the biosonar emission and hearing processes. This paper outlines the methods used in the hearing simulations and offers observations concerning the mechanisms of acoustic reception in this dolphin based on model results. These results include: (1) The left and right mandibular fat bodies were found to channel sound incident from forward directions to the left and right tympanic bulla and to create sharp maxima against the lateral surfaces of each respective bulla; (2) The soft tissues of the lower jaw improved the forward directivity of the simulated receptivity patterns; (3) A focal property of the lower-jaw pan bones appeared to contribute to the creation of distinct forward receptivity peaks for each ear; (4) The reception patterns contained features that may correspond to lateral hearing pathways. A "fast" lens mechanism is proposed to explain the focal contribution of the pan bones in this dolphin. Similar techniques may be used to study hearing in other marine mammals.

  9. Comparison of one-, two-, and three-dimensional models for mass transport of radionuclides

    SciTech Connect

    Prickett, T.A.; Voorhees, M.L.; Herzog, B.L.

    1980-02-01

    This technical memorandum compares one-, two-, and three-dimensional models for studying regional mass transport of radionuclides in groundwater associated with deep repository disposal of high-level radioactive wastes. In addition, this report outlines the general conditions for which a one- or two-dimensional model could be used as an alternate to a three-dimensional model analysis. The investigation includes a review of analytical and numerical models in addition to consideration of such conditions as rock and fluid heterogeneity, anisotropy, boundary and initial conditions, and various geometric shapes of repository sources and sinks. Based upon current hydrologic practice, each review is taken separately and discussed to the extent that the researcher can match his problem conditions with the minimum number of model dimensions necessary for an accurate solution.

  10. Modeling three-dimensional propagation in a continental shelf environment.

    PubMed

    Ballard, Megan S

    2012-03-01

    An acoustic propagation model is applied to predict measurements of three-dimensional (3-D) effects recorded off the southeast coast of Florida. The measured signal is produced by a low frequency source that is towed north parallel to the shelf from a fixed receiving array. The acoustic data show the direct path arrival at the bearing of the tow ship and a second refracted path arrival as much as 30° inshore of the direct arrival. Notably, the refracted arrival has a received level more than 25 dB greater than that of the direct arrival. A geoacoustic model of the environment is created to explain the data. It is shown that the topography of the seafloor plays the largest role in controlling horizontal refraction effects, whereas the range-dependent sediment properties have the most influence on the received level. The modeling approach is based on a 3-D adiabatic mode technique in which the horizontal refraction equation is solved using a parabolic equation in Cartesian coordinates. A modal decomposition of the field provides insight into the variability in the arrival angle and received level of the measured signal.

  11. 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.

  12. Three-Dimensional Oil Dispersion Model in Campos basin, Brazil.

    PubMed

    Oliveira, Bernardo Lopes Almeida de; Netto, Theodoro Antoun; Assad, Luiz Paulo de Freitas

    2017-02-22

    This paper presents the physical and mathematical formulation of a three-dimensional oil dispersion model that calculates the trajectory from the seafloor to the sea surface, its assumptions and constraints. It was developed by researchers that are familiar with oil spill dispersion and mathematical analysis. Oil dispersion is calculated through two computational routines. The first calculates the vertical dispersion along the water column and resamples the droplets when the oil reaches the surface. The second calculates the surface displacement of the spill. This model is based on the Eulerian Approach, and it uses numerical solution schemes in time and in space to solve the equation for advective-diffusive transport. A case study based on an actual accident that happened in the Campos Basin, in Rio de Janeiro State, considering the instant spill of 1.000 m(3) was used to evaluate the proposed model. After calculating the vertical transport, it was estimated that the area covered by the oil spill on the surface was about 35.685 m². After calculating the dispersion at the surface, the plume area was estimated as 20% of the initial area, resulting in a final area of 28.548 m².

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Clubfoot analysis with three-dimensional foot models.

    PubMed

    Song, H R; Carroll, N C; Neyt, J; Carter, J M; Han, J; D'Amato, C R

    1999-01-01

    The purpose of this study was to develop a method of defining, in mathematical terms, the interpositional relationships of the bones of the hindfoot complex in the idiopathic clubfoot and the neurogenic clubfoot. The neurogenic clubfoot and contralateral normal-appearing foot of a stillborn infant with myelomeningocele, and the normal foot of a 10-year-old were sectioned with a cryomicrotome. Magnetic resonance images (MRIs) of the clubfoot and the normal foot of a 3-month-old boy were obtained. Using a computer program, three-dimensional foot models were generated from the digitized cryomicrotome sections and from the MRIs. The central principal axes were determined for the talus and calcaneus. The long central principal axes of the talus and calcaneus were neutrally rotated with reference to the bimalleolar axis in the idiopathic clubfoot while in the neurogenic clubfoot the long central principal axis of the talus was medially rotated 52 degrees and that of the calcaneus 10 degrees. The talocalcaneal angles defined by the long central principal axes in the superior and medial views were 0 degree and 10 degrees, respectively, in the idiopathic clubfoot, and 42 degrees and 56 degrees, respectively, in the neurogenic clubfoot.

  2. Three-dimensional model of magnetized capacitively coupled plasmas

    NASA Astrophysics Data System (ADS)

    Rauf, Shahid; Kenney, Jason; Collins, Ken

    2009-05-01

    A three-dimensional plasma model is used to understand the characteristics of magnetized capacitively coupled plasma discharges. The simulations consider plasmas generated using high frequency (13.5 MHz) and very high frequency (162 MHz) sources, electropositive (Ar) and electronegative (O2) gases, and spatially uniform and nonuniform magnetic fields. Application of a magnetic field parallel to the electrodes is found to enhance the plasma density due to improved electron confinement and shift the plasma due to the E ×B drift. The plasma is electrically symmetric at 162 MHz so it drifts in opposite directions adjacent to the two electrodes due to the E ×B drift. On the other hand, the 13.5 MHz plasma is electrically asymmetric and it predominantly moves in one direction under the influence of the E ×B drift. The E ×B drift focuses the plasma into a smaller volume in regions with convex magnetic field lines. Conversely, the E ×B drift spreads out the plasma in regions with concave magnetic field lines. In a magnetized O2 plasma, the overall plasma is found to move in one direction due to the E ×B drift while the plasma interior moves in the opposite direction. This behavior is linked to the propensity of negative ions to reside in regions of peak plasma potential, which moves closer to the chamber center opposite to the E ×B drift direction.

  3. 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.

  4. 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.

  5. A three-dimensional model of aromatase cytochrome P450.

    PubMed Central

    Graham-Lorence, S.; Amarneh, B.; White, R. E.; Peterson, J. A.; Simpson, E. R.

    1995-01-01

    P450 hemeproteins comprise a large gene superfamily that catalyzes monooxygenase reactions in the presence of a redox partner. Because the mammalian members are, without exception, membrane-bound proteins, they have resisted structure-function analysis by means of X-ray crystallographic methods. Among P450-catalyzed reactions, the aromatase reaction that catalyzes the conversion of C19 steroids to estrogens is one of the most complex and least understood. Thus, to better understand the reaction mechanism, we have constructed a three-dimensional model of P450arom not only to examine the active site and those residues potentially involved in catalysis, but to study other important structural features such as substrate recognition and redox-partner binding, which require examination of the entire molecule (excepting the putative membrane-spanning region). This model of P450arom was built based on a "core structure" identified from the structures of the soluble, bacterial P450s (P450cam, P450terp, and P450BM-P) rather than by molecular replacement, after which the less conserved elements and loops were added in a rational fashion. Minimization and dynamic simulations were used to optimize the model and the reasonableness of the structure was evaluated. From this model we have postulated a membrane-associated hydrophobic region of aliphatic and aromatic residues involved in substrate recognition, a redox-partner binding region that may be unique compared to other P450s, as well as residues involved in active site orientation of substrates and an inhibitor of P450arom, namely vorozole. We also have proposed a scheme for the reaction mechanism in which a "threonine switch" determines whether oxygen insertion into the substrate molecule involves an oxygen radical or a peroxide intermediate. PMID:7549871

  6. Three-Dimensional Analysis and Modeling of a Wankel Engine

    NASA Technical Reports Server (NTRS)

    Raju, M. S.; Willis, E. A.

    1991-01-01

    A new computer code, AGNI-3D, has been developed for the modeling of combustion, spray, and flow properties in a stratified-charge rotary engine (SCRE). The mathematical and numerical details of the new code are described by the first author in a separate NASA publication. The solution procedure is based on an Eulerian-Lagrangian approach where the unsteady, three-dimensional Navier-Stokes equations for a perfect gas-mixture with variable properties are solved in generalized, Eulerian coordinates on a moving grid by making use of an implicit finite-volume, Steger-Warming flux vector splitting scheme. The liquid-phase equations are solved in Lagrangian coordinates. The engine configuration studied was similar to existing rotary engine flow-visualization and hot-firing test rigs. The results of limited test cases indicate a good degree of qualitative agreement between the predicted and measured pressures. It is conjectured that the impulsive nature of the torque generated by the observed pressure nonuniformity may be one of the mechanisms responsible for the excessive wear of the timing gears observed during the early stages of the rotary combustion engine (RCE) development. It was identified that the turbulence intensities near top-dead-center were dominated by the compression process and only slightly influenced by the intake and exhaust processes. Slow mixing resulting from small turbulence intensities within the rotor pocket and also from a lack of formation of any significant recirculation regions within the rotor pocket were identified as the major factors leading to incomplete combustion. Detailed flowfield results during exhaust and intake, fuel injection, fuel vaporization, combustion, mixing and expansion processes are also presented. The numerical procedure is very efficient as it takes 7 to 10 CPU hours on a CRAY Y-MP for one entire engine cycle when the computations are performed over a 31 x16 x 20 grid.

  7. 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.

  8. 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.

  9. 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

  10. Three-Dimensional Multiscale MHD Model of Cometary Plasma Environments

    NASA Technical Reports Server (NTRS)

    Gombosi, Tamas I.; DeZeeuw, Darren L.; Haberli, Roman M.; Powell, Kenneth G.

    1996-01-01

    First results of a three-dimensional multiscale MHD model of the interaction of an expanding cometary atmosphere with the magnetized solar wind are presented. The model starts with a supersonic and super-Alfvenic solar wind far upstream of the comet (25 Gm upstream of the nucleus) with arbitrary interplanetary magnetic field orientation. The solar wind is continuously mass loaded with cometary ions originating from a 10-km size nucleus. The effects of photoionization, electron impact ionization, recombination, and ion-neutral frictional drag are taken into account in the model. The governing equations are solved on an adaptively refined unstructured Cartesian grid using our new multiscale upwind scalar conservation laws-type numerical technique (MUSCL). We have named this the multiscale adaptive upwind scheme for MHD (MAUS-MHD). The combination of the adaptive refinement with the MUSCL-scheme allows the entire cometary atmosphere to be modeled, while still resolving both the shock and the diamagnetic cavity of the comet. The main findings are the following: (1) Mass loading decelerates the solar wind flow upstream of the weak cometary shock wave (M approximately equals 2, M(sub A) approximately equals 2), which forms at a subsolar standoff distance of about 0.35 Gm. (2) A cometary plasma cavity is formed at around 3 x 10(exp 3) km from the nucleus. Inside this cavity the plasma expands outward due to the frictional interaction between ions and neutrals. On the nightside this plasma cavity considerably narrows and a relatively fast and dense cometary plasma beam is ejected into the tail. (3) Inside the plasma cavity a teardrop-shaped inner shock is formed, which is terminated by a Mach disk on the nightside. Only the region inside the inner shock is the 'true' diamagnetic cavity. (4) The model predicts four distinct current systems in the inner coma: the density peak current, the cavity boundary current, the inner shock current, and finally the cross-tail current

  11. 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

  12. 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.

  13. 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.

  14. Three-dimensional modeling of canopy flow in complex terrain

    NASA Astrophysics Data System (ADS)

    Xu, X.; Yi, C.; Montagnani, L.

    2013-12-01

    Flows within and just above forest canopy over mountainous terrain are most complicated, which substantially influence the biosphere-atmosphere interaction of mass and energy. Due to the significant spatial variation, canopy flow in complex terrain is poorly understood based on the point-based tower measurement. We employ numerical model integrated with biogenic CO2 process to examine the impacts of topography, canopy structure, and synoptic atmospheric motion on canopy flow and associated CO2 transport in an alpine forest, with special focus on stable nocturnal condition when biogenic CO2 emission is active. Our model prediction is in better agreement with tower measurements when background synoptic wind is present, which leads to better larger-scale mixing, while local slope flow is just thermal-driven in the modeled domain by ignorance of surround mountain-valley. Our results show that large-scale synoptic wind is modified by local slope-canopy flow within and just above canopy. As the synoptic wind is down-slope (Figure 1a), recirculation is formed on the downwind slope with cool air and high accumulation of CO2 in front of tall and dense vegetation. As the synoptic wind is up-slope(Figure 1b), canopy flow at the higher elevation of the slope is in the same direction of synoptic wind, while canopy flow at the lower part of the slope blows down-slope. The upslope wind causes better mixing in the canopy and leads to smaller CO2 accumulation just close to the slope surface. The local down-slope wind (Figure 1c) causes rich and deep CO2 build-up in the downwind direction on the lower slope. Our numerical performance has demonstrated that three-dimensional CFD approach is a useful tool to understanding relationships between tower-point measurements and surrounding's field distributions. Acknowledgement: This research was supported by NSF Grants ATM-0930015, CNS-0958379 & CNS-0855217, PSC-CUNY ENHC-42-64 & CUNY HPCC. Figure 1 CO2 distribution within and just above

  15. Three-dimensional bioremediation modeling in heterogeneous porous media

    SciTech Connect

    Wheeler, M.F. . Dept. of Mathematical Sciences); Roberson, K.R. ); Chilakapati, A. . Dept. of Chemical Engineering)

    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.

  16. Three-Dimensional Modeling of Guide-Field Magnetic Reconnection

    NASA Technical Reports Server (NTRS)

    Hesse, Michael

    2005-01-01

    The dissipation mechanism of guide field magnetic reconnection remains a subject of intense scientific interest. On one hand, one set of recent studies have shown that particle inertia-based processes, which include thermal and bulk inertial effects, provide the reconnection electric field in the diffusion region. On the other hand, a second set of studies emphasizes the role of wave-particle interactions in providing anomalous resistivity in the diffusion region. In this presentation, we analyze three-dimensional PIC simulations of guide-field magnetic reconnection. Specific emphasis will be on the question whether thermal-inertia processes, mediated by the electron pressure tensor, remain a viable dissipation mechanism in fully three-dimensional systems.

  17. 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.

  18. Mass spectrometry imaging of therapeutics from animal models to three-dimensional cell cultures.

    PubMed

    Liu, Xin; Hummon, Amanda B

    2015-10-06

    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.

  19. 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

  20. 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.

  1. Empirical and accurate method for the three-dimensional electrostatic potential (EM-ESP) of biomolecules.

    PubMed

    Du, Qi-Shi; Wang, Cheng-Hua; Wang, Yu-Ting; Huang, Ri-Bo

    2010-04-01

    The electrostatic potential (ESP) is an important property of interactions within and between macromolecules, including those of importance in the life sciences. Semiempirical quantum chemical methods and classical Coulomb calculations fail to provide even qualitative ESP for many of these biomolecules. A new empirical ESP calculation method, namely, EM-ESP, is developed in this study, in which the traditional approach of point atomic charges and the classical Coulomb equation is discarded. In its place, the EM-ESP generates a three-dimensional electrostatic potential V(EM)(r) in molecular space that is the sum of contributions from all component atoms. The contribution of an atom k is formulated as a Gaussian function g(r(k);alpha(k),beta(k)) = alpha(k)/r(k)(betak) with two parameters (alpha(k) and beta(k)). The benchmark for the parameter optimization is the ESP obtained by using higher-level quantum chemical approaches (e.g., CCSD/TZVP). A set of atom-based parameters is optimized in a training set of common organic molecules. Calculated examples demonstrate that the EM-ESP approach is a vast improvement over the Coulombic approach in producing the molecular ESP contours that are comparable to the results obtained with higher-level quantum chemical methods. The atom-based parameters are shown to be transferrable between one part of closely related aromatic molecules. The atom-based ESP formulization and parametrization strategy can be extended to biological macromolecules, such as proteins, DNA, and RNA molecules. Since ESP is frequently used to rationalize and predict intermolecular interactions, we expect that the EM-ESP method will have important applications for studies of protein-ligand and protein-protein interactions in numerous areas of chemistry, molecular biology, and other life sciences.

  2. 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

  3. 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.

  4. Three dimensional global modeling of atmospheric CO2

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

    The initial attempts to model the atmospheric CO2 distribution, including couplings to the ocean and biosphere as sources and sinks of atmospheric CO2, encourage the notion that this approach will lead to useful quantitative constraints on CO2 fluxes. Realization of this objective will require: (1) continued improvement in the realism of the global transport modeling; (2) extended timeline of atmospheric CO2 monitoring, which improved precision and improved definition of the uncertainties in the measured CO2 amounts; and (3) given an accurate knowledge of model capabilities and limitations and given a good understanding of CO2 observations and their limitations, there is a need for good ideas concerning what quantitative information on the carbon cycle can be inferred from global modeling.

  5. A practical implementation of turbulence models for the computation of three-dimensional separated flows

    NASA Technical Reports Server (NTRS)

    Marx, Yves P.

    1991-01-01

    An upwind MUSCL-type implicit scheme for the three-dimensional Navier-Stokes equations is presented and details on the implementation for three-dimensional flows of a 'diagonal' upwind implicit operator are developed. Turbulence models for separated flows are also described with an emphasis on the numerical specificities of the Johnson-King nonequilibrium model. Good predictions of separated two- and three-dimensional flows are demonstrated.

  6. Fermion bags, duality, and the three dimensional massless lattice thirring model.

    PubMed

    Chandrasekharan, Shailesh; Li, Anyi

    2012-04-06

    The recently proposed fermion-bag approach is a powerful technique to solve some four-fermion lattice field theories. Because of the existence of a duality between strong and weak couplings, the approach leads to efficient Monte Carlo algorithms in both these limits. The new method allows us for the first time to accurately compute quantities close to the quantum critical point in the three dimensional lattice Thirring model with massless fermions on large lattices. The critical exponents at the quantum critical point are found to be ν=0.85(1), η=0.65(1), and η(ψ)=0.37(1).

  7. 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.

  8. 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

  9. Testing a method-of-characteristics model of three-dimensional solute transport in ground water

    USGS Publications Warehouse

    Goode, Daniel J.; Konikow, Leonard F.; ,

    1991-01-01

    A new three-dimensional model of solute transport in groundwater that is based on a widely used two-dimensional method of characteristics model and is coupled to a modular finite-difference flow model is under development. The model's accuracy for ideal aquifers having homogeneous properties, uniform boundary conditions, and steady flow along a grid direction is demonstrated by comparison with conventional analytical solutions. The effect of spatially and temporally variable flow velocities is investigated by comparison with special analytical solutions. To test the performance of the model for typical hydrogeologic conditions, we compare results with those from other models as well as with results from the same model using smaller grid spacings and time steps. This model generally provides accurate results for realistic simulations, and is particularly efficient for advection-dominated transport.

  10. 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

    2014-10-01

    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.

  11. 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

  12. 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.

  13. Three-dimensional single-shot optoacoustic visualization of excised mouse organs with model-based reconstruction

    NASA Astrophysics Data System (ADS)

    Deán-Ben, X. L.; Buehler, Andreas; Ntziachristos, Vasilis; Razansky, Daniel

    2013-03-01

    Optoacoustic imaging offers the unique capability of simultaneous excitation of a three-dimensional (volumetric) region with a single interrogating laser pulse. In this way, three-dimensional imaging with single-shot illumination is theoretically achievable, which in principle allows the visualization of dynamic events at a high frame rate mainly limited by the pulse repetition rate of the laser. Simultaneous acquisition of optoacoustic signals at a set of points surrounding the imaging sample is however required for this purpose, which is hampered by several technical limitations related to lack of appropriate ultrasound detection technology, digital sampling and processing capacities. Also, a convenient reconstruction algorithm must be selected to accurately image the distribution of the optical absorption from the acquired signals. Specifically, the resolution and quantitativeness of the images depend on the reconstruction procedure employed. Herein we describe an accurate three-dimensional model-based optoacoustic reconstruction algorithm based on a convenient discretization of the analytical solution of the forward model. Subsequent algebraic inversion is done with the LSQR algorithm. The performance of the algorithm is showcased by reconstructing an excised mouse heart with a custom made three-dimensional optoacoustic imaging system. In this system, 256 optoacoustic signals corresponding to single-shot excitation are simultaneously collected with an array of ultrasonic transducers disposed on a spherical surface, which allows three-dimensional imaging at a frame rate of 10 Hz.

  14. Three-dimensional Neumann-series approach to model light transport in nonuniform media

    PubMed Central

    Jha, Abhinav K.; Kupinski, Matthew A.; Barrett, Harrison H.; Clarkson, Eric; Hartman, John H.

    2014-01-01

    We present the implementation, validation, and performance of a three-dimensional (3D) Neumann-series approach to model photon propagation in nonuniform media using the radiative transport equation (RTE). The RTE is implemented for nonuniform scattering media in a spherical harmonic basis for a diffuse-optical-imaging setup. The method is parallelizable and implemented on a computing system consisting of NVIDIA Tesla C2050 graphics processing units (GPUs). The GPU implementation provides a speedup of up to two orders of magnitude over non-GPU implementation, which leads to good computational efficiency for the Neumann-series method. The results using the method are compared with the results obtained using the Monte Carlo simulations for various small-geometry phantoms, and good agreement is observed. We observe that the Neumann-series approach gives accurate results in many cases where the diffusion approximation is not accurate. PMID:23201945

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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...

  1. 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.

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

    DOE PAGES

    Tourret, D.; Karma, A.; Clarke, A. J.; ...

    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

  3. 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.

  4. Three-dimensional non-cohesive earthen dam breach model. Part 1: Theory and methodology

    NASA Astrophysics Data System (ADS)

    Wang, Zhengang; Bowles, David S.

    2006-10-01

    An erosion and force/moment equilibrium based three-dimensional dam breach model is developed for the non-cohesive earthen dam overtopping breach problem. The breach location can be anywhere along the dam. The model considers the topography of the entire dam site. Three-dimensional slope stability along the main direction of flow in the breach channel is checked. A second order hybrid-type of total variation diminishing finite-difference scheme is proposed to simulate the dam breach outflow by solving the two-dimensional shallow water equations. The scheme is shown to accurately reproduce supercritical, subcritical, and transcritical flows for the following analytical or experimental cases: one-dimensional theoretical dam break with initially dry and wet beds, steady flow over a bump, hydraulic jump, one-dimensional dam break with a bottom slope, and two-dimensional dam break with bottom and side slopes. Applications to a simple breach channel show that calculated flows match the broad-crested weir formula and reasonably fit the grids.

  5. Three-dimensional osteogenic and chondrogenic systems to model osteochondral physiology and degenerative joint diseases.

    PubMed

    Alexander, Peter G; Gottardi, Riccardo; Lin, Hang; Lozito, Thomas P; Tuan, Rocky S

    2014-09-01

    Tissue engineered constructs have the potential to function as in vitro pre-clinical models of normal tissue function and disease pathogenesis for drug screening and toxicity assessment. Effective high throughput assays demand minimal systems with clearly defined performance parameters. These systems must accurately model the structure and function of the human organs and their physiological response to different stimuli. Musculoskeletal tissues present unique challenges in this respect, as they are load-bearing, matrix-rich tissues whose functionality is intimately connected to the extracellular matrix and its organization. Of particular clinical importance is the osteochondral junction, the target tissue affected in degenerative joint diseases, such as osteoarthritis (OA), which consists of hyaline articular cartilage in close interaction with subchondral bone. In this review, we present an overview of currently available in vitro three-dimensional systems for bone and cartilage tissue engineering that mimic native physiology, and the utility and limitations of these systems. Specifically, we address the need to combine bone, cartilage and other tissues to form an interactive microphysiological system (MPS) to fully capture the biological complexity and mechanical functions of the osteochondral junction of the articular joint. The potential applications of three-dimensional MPSs for musculoskeletal biology and medicine are highlighted.

  6. 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.

  7. Stereographic projection for three-dimensional global discontinuous Galerkin atmospheric modeling

    NASA Astrophysics Data System (ADS)

    Blaise, Sébastien; Lambrechts, Jonathan; Deleersnijder, Eric

    2015-09-01

    A method to solve the three-dimensional compressible Navier-Stokes equations on the sphere is suggested, based on a stereographic projection with a high-order mapping of the elements from the stereographic space to the sphere. The projection is slightly modified, in order to take into account the domain thickness without introducing any approximation about the aspect ratio (deep-atmosphere). In a discontinuous Galerkin framework, the elements alongside the equator are exactly represented using a nonpolynomial geometry, in order to avoid the numerical issues associated with the seam connecting the two hemispheres. This is an crucial point, necessary to avoid mass loss and spurious deviations of the velocity. The resulting model is validated on idealized three-dimensional atmospheric test cases on the sphere, demonstrating the good convergence properties of the scheme, its mass conservation, and its satisfactory behavior in terms of accuracy and low numerical dissipation. A simulation is performed on a variable resolution unstructured grid, producing accurate results despite a substantial reduction of the number of elements.

  8. The First Three Dimensional Digital Models of Shatter Cones

    NASA Astrophysics Data System (ADS)

    Baratoux, D.; Bouley, S.; Reimold, W. U.; Baratoux, L.

    2014-09-01

    Shatter cones are used as a diagnostic evidence for impact, but model of formation is unclear. Geometrical parameters may offer critical tests. The first 3-D models of 30 shatter cones from 16 different impact structures are reported here.

  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. Digital three-dimensional models of Drosophila development.

    PubMed

    Pereanu, Wayne; Hartenstein, Volker

    2004-08-01

    Digital models of organs, cells and subcellular structures have become important tools in biological and medical research. Reaching far beyond their traditional widespread use as didactic tools, computer-generated models serve as electronic atlases to identify specific elements in complex patterns, and as analytical tools that reveal relationships between such pattern elements that would remain obscure in two-dimensional sections. Digital models also offer the unique opportunity to store and display gene-expression patterns, and pilot studies have been made in several genetic model organisms, including mouse, Drosophila and Caenorhabditis elegans, to construct digital graphic databases intended as repositories for gene-expression data.

  12. 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.

  13. 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).

  14. 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.

  15. 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

  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. 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

  18. 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.

  19. 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.

  20. 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.

  1. Three-dimensional environment models from airborne laser radar data

    NASA Astrophysics Data System (ADS)

    Soderman, Ulf; Ahlberg, Simon; Elmqvist, Magnus; Persson, Asa

    2004-09-01

    Detailed 3D environment models for visualization and computer based analyses are important in many defence and homeland security applications, e.g. crisis management, mission planning and rehearsal, damage assessment, etc. The high resolution data from airborne laser radar systems for 3D sensing provide an excellent source of data for obtaining the information needed for many of these models. To utilise the 3D data provided by the laser radar systems however, efficient methods for data processing and environment model construction needs to be developed. In this paper we will present some results on the development of laser data processing methods, including methods for data classification, bare earth extraction, 3D-reconstruction of buildings, and identification of single trees and estimation of their position, height, canopy size and species. We will also show how the results can be used for the construction of detailed 3D environment models for military modelling and simulation applications. The methods use data from discrete return airborne laser radar systems and digital cameras.

  2. The Acceptance of Exceptionality: A Three Dimensional Model.

    ERIC Educational Resources Information Center

    Martin, Larry L.; Nivens, Maryruth K.

    A model extrapolates from E. Kubler-Ross' conception of the stages of grief to apply to parent and family reactions when an exceptionality is identified. A chart lists possible parent feelings and reactions, possible school reactions to the parent in grief, and the child's reactions during each of five stages: denial, rage and anger, bargaining,…

  3. 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.

  4. 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)

  5. 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.

  6. Three-dimensional modeling of high-latitude scintillation observations

    NASA Astrophysics Data System (ADS)

    Chartier, Alex; Forte, Biagio; Deshpande, Kshitija; Bust, Gary; Mitchell, Cathryn

    2016-07-01

    Global Navigation Satellite System signals exhibit rapid fluctuations at high and low latitudes as a consequence of propagation through drifting ionospheric irregularities. We focus on the high-latitude scintillation problem, taking advantage of a conjunction of European Incoherent Scatter Radar (EISCAT) observations and a GPS scintillation monitor viewing the same line of sight. Just after 20:00 UT on 17 October 2013, an auroral E region ionization enhancement occurred with associated phase scintillations. This investigation uses the scintillation observations to estimate the ionospheric electron density distribution beyond the spatial resolution of EISCAT (5-15 km along the line of sight in this case). Following the approach of Deshpande et al. (2014), signal propagation is modeled through a specified density distribution. A multiple phase screen propagation algorithm is applied to irregularities conforming to the description of Costa and Kelley (1977) and constrained to match the macroscopic conditions observed by EISCAT. A 50-member ensemble of modeled outputs is approximately consistent with the observations according to the standard deviation of the phase (σp). The observations have σp = 0.23 rad, while the ensemble of modeled realizations has σp = 0.23 + 0.04-0.04. By comparison of the model output with the scintillation observations, we show that the density fluctuations cannot be a constant fraction of the mean density. The model indicates that E region density fluctuations whose standard deviation varies temporally between 5 and 25% of the mean (EISCAT-observed) density are required to explain the observed phase scintillations.

  7. The influence of patellofemoral joint contact geometry on the modeling of three dimensional patellofemoral joint forces.

    PubMed

    Powers, Christopher M; Chen, Yu-Jen; Scher, Irving; Lee, Thay Q

    2006-01-01

    The purpose of this study was to determine the influence of patellofemoral joint contact geometry on the modeling of three-dimensional patellofemoral joint forces. To achieve this goal, patellofemoral joint reaction forces (PFJRFs) that were measured from an in-vitro cadaveric set-up were compared to PFJRFs estimated from a computer model that did not consider patellofemoral joint contact geometry. Ten cadaver knees were used in this study. Each was mounted on a custom jig that was fixed to an Instron frame. Quadriceps muscle loads were accomplished using a pulley system and weights. The force in the patellar ligament was obtained using a buckle transducer. To quantify the magnitude and direction of the PFJRF, a six-axis load cell was incorporated into the femoral fixation system so that a rigid body assumption could be made. PFJRF data were obtained at 0 degrees , 20 degrees , 40 degrees and 60 degrees of knee flexion. Following in vitro testing, SIMM modeling software was used to develop computational models based on the three-dimensional coordinates (Microscribe digitizer) of individual muscle and patellar ligament force vectors obtained from the cadaver knees. The overall magnitude of the PFJRF estimated from the computer generated models closely matched the direct measurements from the in vitro set-up (Pearson's correlation coefficient, R(2)=0.91, p<0.001). Although the computational model accurately estimated the posteriorly directed forces acting on the joint, some discrepancies were noted in the forces acting in the superior and lateral directions. These differences however, were relatively small when expressed as a total of the overall PFJRF magnitude.

  8. Three-Dimensional Geometric Modeling for Anatomical Structures

    PubMed Central

    Shani, Uri

    1981-01-01

    Computer analysis of images of anatomical structures can benefit from the use of a priori knowledge about the inspected domain. Even though the anatomy structure of humans is variable, it is far more organized than other domains which are commonly used for image understanding (e.g., outdoor scenes or even images of a boxes-and-cylinders world). This paper discusses an organization scheme for modeling the 3-D structure of the abdominal anatomy and its use for analyzing 3-D CAT (Computed Axial Tomography) scans of the abdomen. The discussion is divided into two major portions of the knowledge organization: a relational database for gross anatomy and a 3-D shape model for individual organs using generalized cylinders. The paper also includes an example of 3-D image analysis for the detection of the kidneys' 3-D shape from abdominal CAT scans.

  9. 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.

  10. A three dimensional MHD model of the earth's magnetosphere

    NASA Technical Reports Server (NTRS)

    Wu, C. C.; Walker, R. J.; Dawson, J. M.

    1981-01-01

    The results of a global MHD calculation of the steady state solar wind interaction with a dipole magnetic field are presented. The computer code used, being much faster than previous codes, makes it possible to increase the number of grid points in the system by an order of magnitude. The resulting model qualitatively reproduces many of the observed features of the quiet time magnetosphere including the bow shock, magnetopause, and plasma sheet.

  11. Three-dimensional model of surfactant replacement therapy

    PubMed Central

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

    2015-01-01

    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. PMID:26170310

  12. Engineered three-dimensional multicellular culture model to ...

    EPA Pesticide Factsheets

    Tissue fusion during early mammalian development requires crosstalk between multiple cell types. For example, paracrine signaling between palatal epithelial cells and palatal mesenchyme mediates the fusion of opposing palatal shelves during embryonic development. Fusion events in developmental processes including heart development, neural tube closure, and palatal fusion are dependent on epithelial-mesenchymal interactions (EMIs) and specific signaling pathways that have been elucidated largely using gene knockout mouse models. A broad analysis of literature using ToxRefDB identified 63 ToxCast chemicals associated with cleft palate in animal models. However, the influence of these and other putative teratogens on human palatal fusion has not been examined in depth due to the lack of in vitro models incorporating EMIs between human cell types. We sought to engineer the stratified mesenchymal and epithelial structure of the developing palate in vitro using spheroid culture of human Wharton’s Jelly mesenchymal stem cells (hMSC). hMSC spheroids exhibited uniform size over time (175 ± 21 µm mean diameter) that was proportional to starting cell density. Further, hMSCs in spheroid culture exhibited increased alkaline phosphatase activity and increased expression of bglap and runx2 after 7 days of culture in osteo-induction medium, which suggests that spheroid culture together with osteo-induction medium supports osteogenic differentiation. We developed a novel pro

  13. 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

  14. Three Dimensional Migration and Forward Modelling of Ground Penetrating Radar Data.

    DTIC Science & Technology

    1991-06-01

    Unprocessed Data from the Tesi Pit ..................................................................................... 2 FIGURE 3 3D Migrated Data from...acquisition, and inter - pretation are human driven processes. The potential of GPR to generate accurate three dimensional subsurface maps has not...objects or inter - faces occurred. However, the migration operation causes negative reinforcement in the areas where there are no reflections due to

  15. 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.

  16. 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.

  17. Computational Model of Three Dimensional Elastic Wing Driven by Muscles

    NASA Astrophysics Data System (ADS)

    Wang, Z. Jane; Cowen, Nathaniel; Peskin, Charles S.; Childress, Stephen W.

    2003-11-01

    The flapping wing motion observed in nature results from couplings of muscles, flexible wing structures, and unsteady flows. Previously we have studied the unsteady flows and forces of a rigid two dimensional wing undergoing prescribed motion similar to kinematics observed in insects, as a means of understanding basic unsteady aerodynamic mechanisms. In this talk, we describe our recent progress in constructing a more realistic model insect, which consists of a pair of elastic wings immersed in fluids, and is driven by periodically contracting 'muscles'. A natural computational framework for such a system is the immersed boundary method, which is used here. We present simulations of flapping flight at Reynolds number 10^2, in the same range as that of fruitflies and butterflies.

  18. Development of volcanic passive margins: Three-dimensional laboratory models

    NASA Astrophysics Data System (ADS)

    Callot, Jean-Paul; Geoffroy, Laurent; Brun, Jean-Pierre

    2002-12-01

    Continental breakup above an anomalously hot mantle may lead to the development of volcanic margins. Volcanic margins are characterized by (1) thick seaward dipping lava flow sequences, (2) central intrusive complexes associated with dyke swarms parallel to the coast, and (3) high seismic velocity bodies in the lower crust attributable to magma underplating. A conceptual model for volcanic margins development has recently been proposed based on onshore studies of the Greenland margins and the British Tertiary Igneous Province. It is proposed that the long-lived central intrusions are genetically linked to underlying persistent zones of mantle fusion. These localized melting domains (or soft spots), equivalent to small mantle diapirs, may locally soften the extending continental lithosphere. The low-viscosity diapirs would (1) localize tectonic strain and (2) feed the volcanic margin with magma. Thus such soft spots can control the along-strike magmatic and tectonic segmentation of volcanic margins. Recent geophysical investigations appear to show that the along-strike structure of volcanic passive margins is compatible with such a segmentation process. Here we present a set of scaled experiments designed to study how such localized rheological heterogeneities in the sub-Moho mantle may have a mechanical effect on continental breakup. Four-layer models were constructed using sand and silicone putties to represent the brittle and ductile layers of both crust and mantle. The soft spots are simulated by low-viscosity silicone putty emplaced within the brittle material. At the scale of the entire breakup zone, the soft spots display an oceanic-type strength profile defining low-strength zones where continental breakup is initiated. The rift orientation and segmentation are strongly controlled by the distribution of the low-viscosity heterogeneities, rather than by the direction of regional extension. The experiments are compared with the geometry and segmentation of the

  19. Organotypic three-dimensional culture model of mesenchymal ...

    EPA Pesticide Factsheets

    Tissue fusion during early mammalian development requires coordination of multiple cell types, the extracellular matrix, and complex signaling pathways. Fusion events during processes including heart development, neural tube closure, and palatal fusion are dependent on signaling pathways elucidated using gene knockout mouse models. A broad analysis of literature, ToxRefDB, and ToxCast identified 63 chemicals that are related to cleft palate. However,the influence of these putative teratogens on human palatal fusion has not been studied due to the lack of in vitro models. We sought to engineer the stratified mesenchymal and epithelial structure of the developing palate in vitro via organotypic culture of human mesenchymal stem cell (hMSC) spheroids coated with a single layer of human primary epidermalkeratinocytes (hPEKp). hMSC spheroids exhibited uniform size over time (175 ± 21 µm mean diameter) proportional to starting cell density. Further, we developed a novel procedure to coat hMSC spheroids homogeneously with a single layer of hPEKp cells using a seeding ratio of 0.1-0.2 hPEKp per hMSC, and hMSC/hPEKp spheroids expressed mesenchymal markers (vim+, C044+, CD105+, CD34-) and epithelial markers (krt17+, itga6+) via qRT-PCR. Analysis of adverse outcome pathways related to palate fusion points to an EGF/TGFj33 switch that could be a target for cleft palate teratogens, and both egf and egfr were expressed by hMSC/hPEKp spheres. Finally, hMSCs and hPE

  20. Three-dimensional transient electromagnetic modelling using Rational Krylov methods

    NASA Astrophysics Data System (ADS)

    Börner, Ralph-Uwe; Ernst, Oliver G.; Güttel, Stefan

    2015-09-01

    A computational method is given for solving the forward modelling problem for transient electromagnetic exploration. Its key features are the discretization of the quasi-static Maxwell's equations in space using the first-kind family of curl-conforming Nédélec elements combined with time integration using rational Krylov methods. We show how rational Krylov methods can also be used to solve the same problem in the frequency domain followed by a synthesis of the transient solution using the fast Hankel transform, and we argue that the pure time-domain solution is more efficient. We also propose a new surrogate optimization approach for selecting the pole parameters of the rational Krylov method which leads to convergence within an a priori determined number of iterations independent of mesh size and conductivity structure. These poles are repeated in a cyclic fashion, which, in combination with direct solvers for the discrete problem, results in significantly faster solution times than previously proposed schemes.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Three-dimensional modeling of chloroprene rubber surface topography upon composition

    NASA Astrophysics Data System (ADS)

    Žukienė, Kristina; Jankauskaitė, Virginija; Petraitienė, Stase

    2014-02-01

    In this study the effect of polymer blend composition on the surface roughness has been investigated and simulated. Three-dimensional modeling of chloroprene rubber film surface upon piperylene-styrene copolymer content was conducted. The efficiency of various surface roughness modeling methods, including Monte Carlo, surface growth and proposed method, named as parabolas, were compared. The required parameters for modeling were obtained from atomic force microscopy topographical images of polymer films surface. It was shown that experimental and modeled surfaces have the same correlation function. The quantitative comparison of function parameters was made. It was determined that novel parabolas method is suitable for three-dimensional polymer blends surface roughness description.

  7. 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

  8. 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.

  9. 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.

  10. Evaluation of a Three-Dimensional Chemical Transport Model (PMCAMx) in the Mexico City Metropolitan Area

    NASA Astrophysics Data System (ADS)

    Tsimpidi, A. P.; Karydis, V. A.; Zavala, M.; Lei, W.; Molina, L. T.; Pandis, S. N.

    2007-05-01

    Atmospheric aerosols have adverse effects on human health, contribute to the visibility reduction and influence the energy balance of the planet. A three-dimensional chemical transport model (PMCAMx) (Gaydos et al., 2007) is used to simulate the particular matter (PM) mass composition distribution in the Mexico City Metropolitan Area (MCMA). PMCAMx uses the framework of CAMx (ENVIRON, 2002) modelling the processes of horizontal and vertical advection, horizontal and vertical dispersion, wet and dry deposition, and gas-phase chemistry. In addition to the above, PMCAMx includes three detailed aerosol modules: inorganic aerosol growth (Gaydos et al., 2003; Koo et al., 2003a), aqueous-phase chemistry (Fahey and Pandis, 2001), and secondary organic aerosol formation and growth (Koo et al., 2004). The aerosol thermodynamic model ISORROPIA has been improved as it now simulates explicitly the chemistry of Ca, Mg, and K salts and is linked to PMCAMx. The hybrid approach (Koo et al., 2003b) for modelling aerosol dynamics is applied in order to accurately simulate the inorganic components in coarse mode. This approach assumes that the smallest particles are in equilibrium while the condensation/evaporation equation is solved for the larger ones. The new CMU organic aerosol model, which is based on the splitting of the organic aerosol volatility range in discrete bins, is also used. The model predictions are evaluated against the PM and vapour concentration measurements from the MCMA-2003 Campaign (Molina et al., 2007). References Gaydos, T., Pinder, R., Koo, B., Fahey, Κ., Yarwood, G., and Pandis, S. N., (2007). Development and application of a three-dimensional Chemical Transport Model, PMCAMx. Atmospheric Environment, in press. ENVIRON (2002). User's guide to the comprehensive air quality model with extensions (CAMx). Version 3.10. Report prepared by ENVIRON International corporation, Novato, CA Gaydos, T., Koo, B., and Pandis, S. N., (2003). Development and application of

  11. 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

  12. 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

  13. Coupled Models and Parallel Simulations for Three-Dimensional Full-Stokes Ice Sheet Modeling

    SciTech Connect

    Zhang, Huai; Ju, Lili

    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.

  14. Ultrasonic characterization of three animal mammary tumors from three-dimensional acoustic tissue models

    NASA Astrophysics Data System (ADS)

    Mamou, Jonathan M.

    This dissertation investigated how three-dimensional (3D) tissue models can be used to improve ultrasonic tissue characterization (UTC) techniques. Anatomic sites in tissue responsible for ultrasonic scattering are unknown, which limits the potential applications of ultrasound for tumor diagnosis. Accurate 3D models of tumor tissues may help identify the scattering sites. Three mammary tumors were investigated: a rat fibroadenoma, a mouse carcinoma, and a mouse sarcoma. A 3D acoustic tissue model, termed 3D impedance map (3DZM), was carefully constructed from consecutive histologic sections for each tumor. Spectral estimates (scatterer size and acoustic concentration) were obtained from the 3DZMs and compared to the same estimates obtained with ultrasound. Scatterer size estimates for three tumors were found to be similar (within 10%). The 3DZMs were also used to extract tissue-specific scattering models. The scattering models were found to allow clear distinction between the three tumors. This distinction demonstrated that UTC techniques may be helpful for noninvasive clinical tumor diagnosis.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Three-dimensional computer model for the atmospheric general circulation experiment

    NASA Technical Reports Server (NTRS)

    Roberts, G. O.

    1984-01-01

    An efficient, flexible, three-dimensional, hydrodynamic, computer code has been developed for a spherical cap geometry. The code will be used to simulate NASA's Atmospheric General Circulation Experiment (AGCE). The AGCE is a spherical, baroclinic experiment which will model the large-scale dynamics of our atmosphere; it has been proposed to NASA for future Spacelab flights. In the AGCE a radial dielectric body force will simulate gravity, with hot fluid tending to move outwards. In order that this force be dominant, the AGCE must be operated in a low gravity environment such as Spacelab. The full potential of the AGCE will only be realized by working in conjunction with an accurate computer model. Proposed experimental parameter settings will be checked first using model runs. Then actual experimental results will be compared with the model predictions. This interaction between experiment and theory will be very valuable in determining the nature of the AGCE flows and hence their relationship to analytical theories and actual atmospheric dynamics.

  1. Electric currents in flare ribbons: Observations and three-dimensional standard model

    SciTech Connect

    Janvier, M.; Aulanier, G.; Bommier, V.; Schmieder, B.; Démoulin, P.; Pariat, E.

    2014-06-10

    We present for the first time the evolution of the photospheric electric currents during an eruptive X-class flare, accurately predicted by the standard three-dimensional (3D) flare model. We analyze this evolution for the 2011 February 15 flare using Helioseismic and Magnetic Imager/Solar Dynamics Observatory magnetic observations and find that localized currents in J-shaped ribbons increase to double their pre-flare intensity. Our 3D flare model, developed with the OHM code, suggests that these current ribbons, which develop at the location of extreme ultraviolet brightenings seen with Atmospheric Imaging Assembly imagery, are driven by the collapse of the flare's coronal current layer. These findings of increased currents restricted in localized ribbons are consistent with the overall free energy decrease during a flare, and the shapes of these ribbons also give an indication of how twisted the erupting flux rope is. Finally, this study further enhances the close correspondence obtained between the theoretical predictions of the standard 3D model and flare observations, indicating that the main key physical elements are incorporated in the model.

  2. 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.

  3. Critical phenomena of the majority voter model in a three-dimensional cubic lattice.

    PubMed

    Acuña-Lara, Ana L; Sastre, Francisco

    2012-10-01

    In this work we investigate the critical behavior of the three-dimensional simple-cubic majority voter model. Using numerical simulations and a combination of two different cumulants, we evaluated the critical point with a higher accuracy than the previous numerical result found by Yang, Kim, and Kwak [Phys. Rev. E 77, 051122 (2008)]. Using standard finite-size scaling theory and scaling corrections, we find that the critical exponents ν,γ, and β are the same as those of the three-dimensional Ising model.

  4. Three-dimensional discrete-time Lotka-Volterra models with an application to industrial clusters

    NASA Astrophysics Data System (ADS)

    Bischi, G. I.; Tramontana, F.

    2010-10-01

    We consider a three-dimensional discrete dynamical system that describes an application to economics of a generalization of the Lotka-Volterra prey-predator model. The dynamic model proposed is used to describe the interactions among industrial clusters (or districts), following a suggestion given by [23]. After studying some local and global properties and bifurcations in bidimensional Lotka-Volterra maps, by numerical explorations we show how some of them can be extended to their three-dimensional counterparts, even if their analytic and geometric characterization becomes much more difficult and challenging. We also show a global bifurcation of the three-dimensional system that has no two-dimensional analogue. Besides the particular economic application considered, the study of the discrete version of Lotka-Volterra dynamical systems turns out to be a quite rich and interesting topic by itself, i.e. from a purely mathematical point of view.

  5. Modeling Vehicle Collision Angle in Traffic Crashes Based on Three-Dimensional Laser Scanning Data

    PubMed Central

    Lyu, Nengchao; Huang, Gang; Wu, Chaozhong; Duan, Zhicheng; Li, Pingfan

    2017-01-01

    In road traffic accidents, the analysis of a vehicle’s collision angle plays a key role in identifying a traffic accident’s form and cause. However, because accurate estimation of vehicle collision angle involves many factors, it is difficult to accurately determine it in cases in which less physical evidence is available and there is a lack of monitoring. This paper establishes the mathematical relation model between collision angle, deformation, and normal vector in the collision region according to the equations of particle deformation and force in Hooke’s law of classical mechanics. At the same time, the surface reconstruction method suitable for a normal vector solution is studied. Finally, the estimation model of vehicle collision angle is presented. In order to verify the correctness of the model, verification of multi-angle collision experiments and sensitivity analysis of laser scanning precision for the angle have been carried out using three-dimensional (3D) data obtained by a 3D laser scanner in the collision deformation zone. Under the conditions with which the model has been defined, validation results show that the collision angle is a result of the weighted synthesis of the normal vector of the collision point and the weight value is the deformation of the collision point corresponding to normal vectors. These conclusions prove the applicability of the model. The collision angle model proposed in this paper can be used as the theoretical basis for traffic accident identification and cause analysis. It can also be used as a theoretical reference for the study of the impact deformation of elastic materials. PMID:28264517

  6. Modeling Vehicle Collision Angle in Traffic Crashes Based on Three-Dimensional Laser Scanning Data.

    PubMed

    Lyu, Nengchao; Huang, Gang; Wu, Chaozhong; Duan, Zhicheng; Li, Pingfan

    2017-02-28

    In road traffic accidents, the analysis of a vehicle's collision angle plays a key role in identifying a traffic accident's form and cause. However, because accurate estimation of vehicle collision angle involves many factors, it is difficult to accurately determine it in cases in which less physical evidence is available and there is a lack of monitoring. This paper establishes the mathematical relation model between collision angle, deformation, and normal vector in the collision region according to the equations of particle deformation and force in Hooke's law of classical mechanics. At the same time, the surface reconstruction method suitable for a normal vector solution is studied. Finally, the estimation model of vehicle collision angle is presented. In order to verify the correctness of the model, verification of multi-angle collision experiments and sensitivity analysis of laser scanning precision for the angle have been carried out using three-dimensional (3D) data obtained by a 3D laser scanner in the collision deformation zone. Under the conditions with which the model has been defined, validation results show that the collision angle is a result of the weighted synthesis of the normal vector of the collision point and the weight value is the deformation of the collision point corresponding to normal vectors. These conclusions prove the applicability of the model. The collision angle model proposed in this paper can be used as the theoretical basis for traffic accident identification and cause analysis. It can also be used as a theoretical reference for the study of the impact deformation of elastic materials.

  7. 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.

  8. An Easy Semantic Differential Technique: Construction of a Three-Dimensional Model.

    ERIC Educational Resources Information Center

    Lawson, E. D.

    Osgood, Suci, and Tannenbaum in their work with the semantic differential developed a technique with which data from an individual could be represented by a three-dimensional model. The model is derived from distance scores based upon profile ratings of concepts such as mother or self, on subscales such as kind-cruel, weak-strong, etc. Osgood…

  9. 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...

  10. Finite-element model for three-dimensional optical scattering problems.

    PubMed

    Wei, Xiuhong; Wachters, Arthur J; Urbach, H Paul

    2007-03-01

    We present a three-dimensional model based on the finite-element method for solving the time-harmonic Maxwell equation in optics. It applies to isotropic or anisotropic dielectrics and metals and to many configurations such as an isolated scatterer in a multilayer, bi-gratings, and crystals. We discuss the application of the model to near-field optical recording.

  11. Three-dimensional (3D) printed endovascular simulation models: a feasibility study

    PubMed Central

    Nesbitt, Craig; McCaslin, James; Bagnall, Alan; Davey, Philip; Bose, Pentop; Williams, Rob

    2017-01-01

    Background Three-dimensional (3D) printing is a manufacturing process in which an object is created by specialist printers designed to print in additive layers to create a 3D object. Whilst there are initial promising medical applications of 3D printing, a lack of evidence to support its use remains a barrier for larger scale adoption into clinical practice. Endovascular virtual reality (VR) simulation plays an important role in the safe training of future endovascular practitioners, but existing VR models have disadvantages including cost and accessibility which could be addressed with 3D printing. Methods This study sought to evaluate the feasibility of 3D printing an anatomically accurate human aorta for the purposes of endovascular training. Results A 3D printed model was successfully designed and printed and used for endovascular simulation. The stages of development and practical applications are described. Feedback from 96 physicians who answered a series of questions using a 5 point Likert scale is presented. Conclusions Initial data supports the value of 3D printed endovascular models although further educational validation is required. PMID:28251121

  12. 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.

  13. Three-dimensional modelling of calving processes on Johnsons Glacier, Livingston Island, Antarctica

    NASA Astrophysics Data System (ADS)

    Otero, Jaime; Navarro, Francisco J.; Martín, Carlos; Cuadrado, M. Luisa; Corcuera, M. Isabel

    2010-05-01

    Iceberg calving is an important mass loss mechanism from ice shelves and tidewater glaciers for many mid- and high-latitude glaciers and ice caps, yet the process is not well represented in prognostic models of ice dynamics. Benn and others (2007) proposed a calving criterion appropriate for both grounded and floating glacier tongues or ice shelves. This criterion assumes that the calving is triggered by the downward propagation of transverse surface crevasses, near the calving front, as a result of the extensional stress regime. The crevasse depth is calculated following Nye (1957), assuming that the base of a field of closely spaced crevasses lies at a depth where the longitudinal tensile strain rate tending to open the crevasse equals the creep closure resulting from the ice overburden pressure. Crevasses partially or totally filled with water will penetrate deeper, because of the contribution of water pressure to the opening of the crevasse. This criterion is readily incorporated into glacier and ice sheet models, but has not been fully validated with observations. We apply a three-dimensional extension of Benn and others' (2007) criterion, incorporated into a full-Stokes model of glacier dynamics, to estimate the current position of the calving front of Johnsons Glacier, Antarctica. We develop four experiments: (i) an straightforward three-dimensional extension of Benn and other's (2007) model; (2) an improvement to the latter that computes the tensile deviatoric stress opening the crevasse using the full-stress solution; (iii) a further improvement based on finding the depth at which the model-computed tensile deviatoric stress, considered as a function of depth, equals the ice overburden closure pressure; (iv) an experiment that adds, to the above, the effect of a threshold strain rate required for crevasses initiation. We found that the improvements considered in experiments (ii) and (iii) were necessary to reproduce accurately the observed calving front

  14. Three-dimensional finite element modeling of a magnet array spinning above a conductor

    NASA Astrophysics Data System (ADS)

    Lorimer, W. L.; Lieu, D. K.; Hull, J. R.; Mulcahy, T. M.; Rossing, T. D.

    Drag forces due to eddy currents induced by the relative motion of a conductor and a magnetic field occur in many practical devices: motors, brakes, magnetic bearings, and magnetically levitated vehicles. Recently, finite element codes have included solvers for three dimensional eddy current geometries and have the potential to be very useful in the design and analysis of these devices. In this paper, numerical results from three dimensional modeling of a magnet array spinning above a conductor are compared to experimental results in order to assess the capabilities of these codes.

  15. Three-dimensional modeling of electron quasiviscous dissipation in guide-field magnetic reconnection

    SciTech Connect

    Hesse, Michael; Kuznetsova, Masha; Schindler, Karl; Birn, Joachim

    2005-10-01

    A numerical study of guide-field magnetic reconnection in a three-dimensional model is presented. Starting from an initial, perturbed, force-free current sheet, it is shown that reconnection develops to an almost translationally invariant state, where magnetic perturbations are aligned primarily along the main current flow direction. An analysis of guide-field and electron flow signatures indicates behavior that is very similar to earlier, albeit not three-dimensional, simulations. Furthermore, a detailed investigation of electron pressure nongyrotropies in the central diffusion region confirms the major role the associated dissipation process plays in establishing the reconnection electric field.

  16. 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

  17. Using Three-dimensional Plant Root Architecture in Models of Shallow-slope Stability

    PubMed Central

    Danjon, Frédéric; Barker, David H.; Drexhage, Michael; Stokes, Alexia

    2008-01-01

    Background The contribution of vegetation to shallow-slope stability is of major importance in landslide-prone regions. However, existing slope stability models use only limited plant root architectural parameters. This study aims to provide a chain of tools useful for determining the contribution of tree roots to soil reinforcement. Methods Three-dimensional digitizing in situ was used to obtain accurate root system architecture data for mature Quercus alba in two forest stands. These data were used as input to tools developed, which analyse the spatial position of roots, topology and geometry. The contribution of roots to soil reinforcement was determined by calculating additional soil cohesion using the limit equilibrium model, and the factor of safety (FOS) using an existing slope stability model, Slip4Ex. Key Results Existing models may incorrectly estimate the additional soil cohesion provided by roots, as the spatial position of roots crossing the potential slip surface is usually not taken into account. However, most soil reinforcement by roots occurs close to the tree stem and is negligible at a distance >1·0 m from the tree, and therefore global values of FOS for a slope do not take into account local slippage along the slope. Conclusions Within a forest stand on a landslide-prone slope, soil fixation by roots can be minimal between uniform rows of trees, leading to local soil slippage. Therefore, staggered rows of trees would improve overall slope stability, as trees would arrest the downward movement of soil. The chain of tools consisting of both software (free for non-commercial use) and functions available from the first author will enable a more accurate description and use of root architectural parameters in standard slope stability analyses. PMID:17766845

  18. 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

  19. Correlation of experimental data and three-dimensional finite element modeling of a spinning quadrupole

    NASA Astrophysics Data System (ADS)

    Lorimer, W. L.; Lieu, D. K.; Hull, J. R.; Mulcahy, T. M.; Rossing, T. D.

    A permanent magnet quadrupole spinning over an aluminum disk was constructed, and drag torque was measured for various speeds and gap sizes. The experiment was modeled using a three-dimensional finite element program. Experimental and analytical results were compared, and the effect of magnet polarity was determined.

  20. Scale invariance implies conformal invariance for the three-dimensional Ising model.

    PubMed

    Delamotte, Bertrand; Tissier, Matthieu; Wschebor, Nicolás

    2016-01-01

    Using the Wilson renormalization group, we show that if no integrated vector operator of scaling dimension -1 exists, then scale invariance implies conformal invariance. By using the Lebowitz inequalities, we prove that this necessary condition is fulfilled in all dimensions for the Ising universality class. This shows, in particular, that scale invariance implies conformal invariance for the three-dimensional Ising model.

  1. Numerical evidence of spin-chirality decoupling in the three-dimensional heisenberg spin glass model.

    PubMed

    Viet, Dao Xuan; Kawamura, Hikaru

    2009-01-16

    Ordering of the three-dimensional Heisenberg spin glass with Gaussian coupling is studied by extensive Monte Carlo simulations. The model undergoes successive chiral-glass and spin-glass transitions at nonzero temperatures T_{CG}>T_{SG}>0, exhibiting spin-chirality decoupling.

  2. 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...

  3. 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.

  4. 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.

  5. 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.

  6. A model for the three-dimensional spacecraft control laboratory experiment

    NASA Technical Reports Server (NTRS)

    Kakad, Yogendra P.

    1991-01-01

    A model for the three-dimensional Spacecraft Control Laboratory Experiment (SCOLE) is developed. The objective behind this method of modelling is to utilize the basic partial differential equations of motion for this distributed parameter system and not to use the modal expansion in developing the model. The final model obtained is in terms of a transfer function matrix which relates the flexible mast parameters like displacement, slope, shear stress, etc. to external forces and moments.

  7. 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.

  8. Computational analysis of three-dimensional epithelial morphogenesis using vertex models

    PubMed Central

    Du, XinXin; Osterfield, Miriam; Shvartsman, Stanislav Y.

    2014-01-01

    The folding of epithelial sheets, accompanied by cell shape changes and rearrangements, gives rise to three-dimensional structures during development. Recently, some aspects of epithelial morphogenesis have been modeled using vertex models, in which each cell is approximated by a polygon; however, these models have been largely confined to two dimensions. Here, we describe an adaptation of these models in which the classical two-dimensional vertex model is embedded in three dimensions. This modification allows for the construction of complex three-dimensional shapes from simple sheets of cells. We describe algorithmic, computational, and biophysical aspects of our model, with the view that it may be useful for formulating and testing hypotheses regarding the mechanical forces underlying a wide range of morphogenetic processes. PMID:25410646

  9. A three-dimensional constitutive model for magnetic shape memory alloys under magneto-mechanical loadings

    NASA Astrophysics Data System (ADS)

    Mousavi, Mohammad Reza; Arghavani, Jamal

    2017-01-01

    This paper presents a three-dimensional phenomenological constitutive model for magnetic shape memory alloys (MSMAs), developed within the framework of irreversible continuum thermodynamics. To this end, a proper set of internal variables is introduced to reflect the microstructural consequences on the material macroscopic behavior. Moreover, a stress-dependent thermodynamic force threshold for variant reorientation is introduced which improves the model accuracy. Preassumed kinetic equations for magnetic domain volume fractions, decoupled equations for magnetization unit vectors and appropriate presentation of the limit function for martensite variant reorientation lead to a simple formulation of the proposed constitutive model. To show the model capability in reproducing the main features of MSMAs, several numerical examples are solved and compared with available experimental data as well as available three-dimensional constitutive models in the literature. Demonstrating good agreement with experimental data besides possessing computational advantages, the proposed constitutive model can be used for analysis of MSMA-based smart structures.

  10. Three-dimensional Modelling Technology for City Indoor Positioning and Navigation Applications

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Chen, Yongxin; Wang, Weisheng

    2016-11-01

    For city indoor positioning and navigation applications, there are two technical problems should be solved, which are the modelling efficiency and the validity and accuracy of the spatial models. In this paper, the quick modelling technology is introduced which uses the multi-angle remote sensing based on the unmanned aerial vehicle measurement. To enhance the validity and accuracy of the spatial models, we proposed an algorithm to remove the line style and planar style foreground occlusions before reconstructing backgrounds. The three-dimensional models can only provide the spatial framework for the city indoor positioning. Furthermore, the simple indoor three-dimensional modelling technology which is based on the building design drawings. In the end, the application in the public safety emergency rescue is introduced.

  11. 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.

  12. Design Recommendations for the Smart Weapons Operability Enhancement Three-Dimensional Thermal Model.

    DTIC Science & Technology

    1991-11-26

    PAGES 44 BTI /SWOE, 3-D Thermal models 16. PRICE CODE 17. SECURITY CLASSIFICATION 18. SECURITY CLASSIFICATION 19. SECURITY CLASSIFICATION 20. UMITATION...Enhancement Three-Dimensional Thermal Model 1 INTRODUCTION 1.1 Background and Purpose of Research The Balanced Technology Initiative ( BTI ) on Smart...dimensional (1-D) thermal models was performed’ for the BTI /SWOE ! Balick, LK., Hummel, J.R., Smith, J.A., and Kimes, D.S. (1990) "One Dimensional

  13. 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

  14. Development and Application of a Three-Dimensional Finite Element Vapor Intrusion Model

    PubMed Central

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

    2010-01-01

    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

  15. 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.

  16. A Three-Dimensional Computational Human Head Model That Captures Live Human Brain Dynamics.

    PubMed

    Ganpule, Shailesh; Daphalapurkar, Nitin P; Ramesh, Kaliat T; Knutsen, Andrew K; Pham, Dzung L; Bayly, Philip V; Prince, Jerry L

    2017-04-10

    Diffuse axonal injury (DAI) is a debilitating consequence of traumatic brain injury (TBI) attributed to abnormal stretching of axons caused by blunt head trauma or acceleration of the head. We developed an anatomically accurate, subject-specific, three-dimensional (3D) computational model of the human brain, and used it to study the dynamic deformations in the substructures of the brain when the head is subjected to rotational accelerations. The computational head models use anatomy and morphology of the white matter fibers obtained using MRI. Subject-specific full-field shearing motions in live human brains obtained through a recently developed tagged MRI imaging technique are then used to validate the models by comparing the measured and predicted heterogeneous dynamic mechanical response of the brain. These results are used to elucidate the dynamics of local shearing deformations in the brain substructures caused by rotational acceleration of the head. Our work demonstrates that the rotational dynamics of the brain has a timescale of ∼100 ms as determined by the shearing wave speeds, and thus the injuries associated with rotational accelerations likely occur over these time scales. After subject-specific validation using the live human subject data, a representative subject-specific head model is used to simulate a real life scenario that resulted in a concussive injury. Results suggest that regions of the brain, in the form of a toroid, encompassing the white matter, the cortical gray matter, and outer parts of the limbic system have a higher susceptibility to injury under axial rotations of the head.

  17. A three-dimensional chemo-mechanical continuum model for smooth muscle contraction.

    PubMed

    Böl, Markus; Schmitz, André; Nowak, Götz; Siebert, Tobias

    2012-09-01

    Based on two fields, namely the placement and the calcium concentration, a chemo-mechanically coupled three-dimensional model, describing the contractile behaviour of smooth muscles, is presented by means of a strain energy function. The strain energy function (Schmitz and Böl, 2011) is additively decomposed into a passive part, relating to elastin and collagen, and an active calcium-driven part related to the chemical contraction of the smooth muscle cells. For the description of the calcium phase the four state cross-bridge model of Hai and Murphy (Hai and Murphy, 1988) has been implemented into the finite element method. Beside three-dimensional illustrative boundary-value problems demonstrating the features of the presented modelling concept, simulations on an idealised artery document the applicability of the model to more realistic geometries.

  18. Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier.

    PubMed

    Lopreore, Courtney L; Bartol, Thomas M; Coggan, Jay S; Keller, Daniel X; Sosinsky, Gina E; Ellisman, Mark H; Sejnowski, Terrence J

    2008-09-15

    A computational model is presented for the simulation of three-dimensional electrodiffusion of ions. Finite volume techniques were used to solve the Poisson-Nernst-Planck equation, and a dual Delaunay-Voronoi mesh was constructed to evaluate fluxes of ions, as well as resulting electric potentials. The algorithm has been validated and applied to a generalized node of Ranvier, where numerical results for computed action potentials agree well with cable model predictions for large clusters of voltage-gated ion channels. At smaller channel clusters, however, the three-dimensional electrodiffusion predictions diverge from the cable model predictions and show a broadening of the action potential, indicating a significant effect due to each channel's own local electric field. The node of Ranvier complex is an elaborate organization of membrane-bound aqueous compartments, and the model presented here represents what we believe is a significant first step in simulating electrophysiological events with combined realistic structural and physiological data.

  19. A new three-dimensional terrain-following tidal model of free-surface flows

    NASA Astrophysics Data System (ADS)

    Lu, Fuqiang; Zhang, Zhuo; Song, Zhiyao; Yue, Songshan; Wen, Yongning

    2015-12-01

    A three-dimensional hydrodynamic model is presented which combines a terrain-following vertical coordinate with a horizontally orthogonal curvilinear coordinate system to fit the complex bottom topography and coastlines near estuaries, continental shelves, and harbors. To solve the governing equations more efficiently, we improve the alternating direction implicit method, which is extensively used in the numerical modeling of horizontal two-dimensional shallow water equations, and extend it to a three-dimensional tidal model with relatively little computational effort. Through several test cases and realistic applications, as presented in the paper, it can be demonstrated that the model is capable of simulating the periodic to-and-fro currents, wind-driven flow, Ekman spirals, and tidal currents in the near-shore region.

  20. 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.

  1. Three-dimensional turbulent relative dispersion by the Gledzer-Ohkitani-Yamada shell model

    NASA Astrophysics Data System (ADS)

    Chakraborty, Sagar; Jensen, Mogens H.; Madsen, Bo S.

    2010-01-01

    We study pair dispersion in a three-dimensional incompressible high Reynolds number turbulent flow generated by Fourier transforming the dynamics of the Gledzer-Ohkitani-Yamada (GOY) shell model into real space. We show that GOY shell model can successfully reproduce both the Batchelor and the Richardson-Obukhov regimes of turbulent relative dispersion. We also study how the crossover time scales with the initial separations of a particle pair and compare it to the prediction by Batchelor.

  2. 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)

  3. 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

  4. A quasi-three-dimensional model for intra-stator transport of rotor wakes

    NASA Astrophysics Data System (ADS)

    Ng, W. F.; Epstein, A. H.

    The time-resolved flowfield in a high thru-flow compressor stage has been studied using a higher frequency response angle probe and a newly developed time-resolved total temperature and pressure probe. The investigation revealed the presence of large gapwise nonuniformity (20C) in stagnation temperature at the stator exit. A quasi-three-dimensional wake transport model, modified from that developed by Kerrebrock and Mikolajczak, was used to investigate the transport of the wake fluid within the stator passage. The present model accounts for three-dimensional effect by including the radial velocity in the wake. In addition, the relative flow angle is not assumed to be uniform across the wake and the inviscid core. The model compares favorably with measurements taken at the stator exit plane. The loss associated with the recirculation of the rotor wake within the stator passage is also calculated.

  5. Three-Dimensional Printing of a Hemorrhagic Cervical Cancer Model for Postgraduate Gynecological Training

    PubMed Central

    Ryan, Stephen; Doucet, Gregory; Murphy, Deanna; Turner, Jacqueline

    2017-01-01

    Introduction A realistic hemorrhagic cervical cancer model was three-dimensionally (3D) printed and used in a postgraduate medical simulation training session. Materials and methods Computer-assisted design (CAD) software was the platform of choice to create and refine the cervical model. Once the prototype was finalized, another software allowed for the addition of a neoplastic mass, which included openings for bleeding from the neoplasm and cervical os. 3D printing was done using two desktop printers and three different materials. An emergency medicine simulation case was presented to obstetrics and gynecology residents who were at varying stages of their training. The scenario included history taking and physical examination of a standardized patient. This was a hybrid simulation; a synthetic pelvic task trainer that allowed the placement of the cervical model was connected to the standardized patient. The task trainer was placed under a drape and appeared to extend from the standardized patient’s body. At various points in the simulation, the standardized patient controlled the cervical bleeding through a peripheral venous line. Feedback forms were completed, and the models were discussed and evaluated with staff. Results A final cervical model was created and successfully printed. Overall, the models were reported to be similar to a real cervix. The models bled well. Most models were not sutured during the scenarios, but overall, the value of the printed cervical models was reported to be high. Discussion The models were well received, but it was suggested that more colors be integrated into the cervix in order to better emphasize the intended pathology. The model design requires further improvement, such as the addition of a locking mechanism, in order to ensure that the cervix stays inside the task trainer throughout the simulation. Adjustments to the simulated blood product would allow the bleeding to flow more vigorously. Additionally

  6. A non-delta-chrome OPC methodology for process models with three-dimensional mask effects

    NASA Astrophysics Data System (ADS)

    Ng, Philip C. W.; Tsai, Kuen-Yu; Tang, Chih-Hsien; Melvin, Lawrence

    2010-04-01

    Delta-chrome optical proximity correction (OPC) has been widely adopted in lithographic patterning for semiconductor manufacturing. During the delta-chrome OPC iteration, a predetermined amount of chrome is added or subtracted from the mask pattern. With this chrome change, the change of exposure intensity error (IE) or the change of edge placement error (EPE) between the printed contour and the target pattern is then calculated based on standard Kirchhoff approximation. Linear approximation is used to predict the amount of the proper chrome change to remove the correction error. This approximation can be very fast and effective, but must be performed iteratively to capture interactions between chrome changes. As integrated circuit (IC) design shrinks to the deep sub-wavelength regime, previously ignored nonlinear process effects, such as three-dimensional (3D) mask effects and resist development effects, become significant for accurate prediction and correction of proximity effects. These nonlinearities challenge the deltachrome OPC methodology. The model response to mask pattern perturbation by linear approximation can be readily computed but inaccurate. In fact, computation of the mask perturbation response becomes complex and expensive. A non-delta-chrome OPC methodology with IE-based feedback compensation is proposed. It determines the amount of the proper chrome change based on IE without intensive computation of mask perturbation response. Its effectiveness in improving patterning fidelity and runtime is examined on a 50-nm practical circuit layout. Despite the presence and the absence of nonlinear 3D mask effects, our results show the proposed non-delta-chrome OPC outperforms the deltachrome one in terms of patterning fidelity and runtime. The results also demonstrate that process models with 3D mask effects limit the use of delta-chrome OPC methodology.

  7. Comparison of GPS Data From the Ventura Basin, California to Interseismic Three-Dimensional Mechanical Models

    NASA Astrophysics Data System (ADS)

    Marshall, S. T.; Cooke, M. L.; Owen, S.

    2005-12-01

    Geodetic data from the Southern California Integrated Geodetic Network (SCIGN) provide information on interseismic deformation patterns in the Ventura Basin, which can be compared to results from three-dimensional mechanical models. This comparison may determine the most realistic among differing three-dimensional active fault configurations and predict slip rates for unconstrained faults. Although the Ventura basin is one of the fastest converging areas within southern California, geodetic signals are complicated by seasonal fluid injection/withdrawal. We use geodetic data that has been corrected for seasonal anthropomorphic effects for comparison to a set of three-dimensional mechanical models. For our models, we use three-dimensional triangulated fault surfaces defined by the Community Fault Model (CFM) for the Ventura Basin. Fault surfaces from the CFM have been modified to extend below the seismogenic portion of the crust (depth < 18 km) to a 27 km deep freely-slipping horizontal crack representing the Mohorovic Discontinuity. We establish two sets of Boundary Element Method (BEM) models, one with 149 - remote contraction determined from relative displacement of distal SCIGN stations and one with N-S contraction, similar to tectonic boundary conditions of the nearby Los Angeles basin. For each set of tectonic boundary conditions, we calculate fault slip rates over a simulated period of 5000 years, which should exceed the recurrence intervals for all faults. Within each model, the greater compliance of the 6 km deep sedimentary basin, relative to the surrounding basement, is simulated by a network of small randomly oriented cracks. The density and length of cracks is chosen to approximate the stiffness of sedimentary material under the applied strain rates. For validation of the three-dimensional model and tectonic boundary conditions, fault slip rates and rakes are calculated and are compared to available paleoseismic rates. Our results suggest that model

  8. Structure optimization in a three-dimensional off-lattice protein model.

    PubMed

    Huang, Wenqi; Liu, Jingfa

    2006-06-05

    We studied a three-dimensional off-lattice AB model with two species of monomers, hydrophobic (A) and hydrophilic (B), and present two optimization algorithms: face-centered-cubic (FCC)-lattice pruned-enriched-Rosenbluth method (PERM) and subsequent conjugate gradient (PERM++) minimization and heuristic conjugate gradient (HCG) simulation based on "off-trap" strategy. In PERM++, we apply the PERM to the FCC-lattice to produce the initial conformation, and conjugate gradient minimization is then used to reach the minimum energy state. Both algorithms have been tested in the three-dimensional AB model for all sequences with lengths 13 < or = n < or = 55. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we renew the putative ground states energy values.

  9. Slicing the three-dimensional Ising model: Critical equilibrium and coarsening dynamics.

    PubMed

    Arenzon, Jeferson J; Cugliandolo, Leticia F; Picco, Marco

    2015-03-01

    We study the evolution of spin clusters on two-dimensional slices of the three-dimensional Ising model in contact with a heat bath after a sudden quench to a subcritical temperature. We analyze the evolution of some simple initial configurations, such as a sphere and a torus, of one phase embedded into the other, to confirm that their area disappears linearly with time and to establish the temperature dependence of the prefactor in each case. Two generic kinds of initial states are later used: equilibrium configurations either at infinite temperature or at the paramagnetic-ferromagnetic phase transition. We investigate the morphological domain structure of the coarsening configurations on two-dimensional slices of the three-dimensional system, compared with the behavior of the bidimensional model.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Exact solution of three-dimensional transport problems using one-dimensional models. [in semiconductor devices

    NASA Technical Reports Server (NTRS)

    Misiakos, K.; Lindholm, F. A.

    1986-01-01

    Several parameters of certain three-dimensional semiconductor devices including diodes, transistors, and solar cells can be determined without solving the actual boundary-value problem. The recombination current, transit time, and open-circuit voltage of planar diodes are emphasized here. The resulting analytical expressions enable determination of the surface recombination velocity of shallow planar diodes. The method involves introducing corresponding one-dimensional models having the same values of these parameters.

  16. 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.

  17. Computer aided shot reconstructions by means of individualized animated three-dimensional victim models.

    PubMed

    Subke, Jörg; Haase, Sibylle; Wehner, Heinz Dieter; Wehner, Frank

    2002-02-18

    In cases of lethal firearm injuries with indefinite indications concerning self-versus third-party infliction a computer enhanced reconstruction with the aim of an anatomical feasibility study can provide significant clues concerning the course of the traumatic event. To this end an exact three-dimensional geometrical model of the victim including all relevant anatomical data as well as the careful documentation of the injuries and a three-dimensional model of the characteristic outlines of the weapon true to scale is generated with the help of an animation program (POSER Version 4, Meta Creation, Egisys AG). With this animated digital three-dimensional model of the victim and the weapon a series of simulation sequences is created by variation of the body positions and the grasp of the weapon. Anatomically impossible positions in view of the physical characteristics of the victim and the site and direction of the bullet path are automatically excluded from the reconstruction. An exact match of the simulation sequence and the real injuries is a statement for a possible self-infliction of the gunshot wound.

  18. 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.

  19. 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.

  20. Using three-dimensional protein structure to model protein aggregation: Collagen fibrillogenesis in vitro

    NASA Astrophysics Data System (ADS)

    Anderson, Darren; Graovac, Ivan; Rainey, Jan; Goh, M. Cynthia

    2004-03-01

    Collagen is the most prevalent protein in mammals. In vitro, it self-assembles into a variety of fibrillar constructs which depend on solution conditions. These assembly processes are still not understood in a thorough manner, in part because of the lack of a three-dimensional structure of the rather large monomer ( 3000 amino acids). Using a statistically-based reduced-rotamer representation alongside a triple-helical backbone parameterization, we have created a 3-D collagen model, and examined the location of charges as a function of pH. Using this representation, we propose a mechanism of assembly that accounts for the morphology (observed using atomic force microscopy) of the most common fibrillar construct. Furthermore, we demonstrate that the experimentally observed effects of pH and ionic strength on the assembly process can be related to the three-dimensional structure of the monomer.

  1. 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.

  2. Time-accurate anisotropic mesh adaptation for three-dimensional time-dependent problems with body-fitted moving geometries

    NASA Astrophysics Data System (ADS)

    Barral, N.; Olivier, G.; Alauzet, F.

    2017-02-01

    Anisotropic metric-based mesh adaptation has proved its efficiency to reduce the CPU time of steady and unsteady simulations while improving their accuracy. However, its extension to time-dependent problems with body-fitted moving geometries is far from straightforward. This paper establishes a well-founded framework for multiscale mesh adaptation of unsteady problems with moving boundaries. This framework is based on a novel space-time analysis of the interpolation error, within the continuous mesh theory. An optimal metric field, called ALE metric field, is derived, which takes into account the movement of the mesh during the adaptation. Based on this analysis, the global fixed-point adaptation algorithm for time-dependent simulations is extended to moving boundary problems, within the range of body-fitted moving meshes and ALE simulations. Finally, three dimensional adaptive simulations with moving boundaries are presented to validate the proposed approach.

  3. 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…

  4. 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.

  5. Three-dimensional modeling of flow and deformation in idealized mild and moderate arterial vessels.

    PubMed

    Gu, Xi; Yeoh, Guan Heng; Timchenko, Victoria

    2016-10-01

    Three-dimensional numerical calculations of mild and moderate stenosed blood vessels have been performed. Large eddy simulation through a dynamic subgrid scale Smagorinsky model is applied to model the transitional and turbulent pulsatile flow. For the compliant stenosed model, fluid-structure interaction is realized through a two-way coupling between the fluid flow and the deforming vessel through the change in the external diameter due to the increment of circumferential pressure via a novel moving boundary approach. Model predictions compare very well against measured and numerical data for the centerline velocities, thickness of the flow separation zones and radial wall displacements.

  6. 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.

  7. 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.

  8. 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.

  9. A three-dimensional thermal and electromagnetic model of whole limb heating with a MAPA.

    PubMed

    Charny, C K; Levin, R L

    1991-10-01

    Previous studies by the authors have shown that if properly implemented, the Pennes assumptions can be applied to quantify bioheat transfer during extremity heating. Given its relative numerical simplicity and its ability to predict temperatures in thermoregulated tissue, the Pennes model of bioheat transfer was utilized in a three-dimensional thermal model of limb heating. While the arterial blood temperature was assumed to be radially uniform within a cross section of the limb, axial gradients in the arterial and venous blood temperatures were computed with this three-dimensional model. A realistically shaped, three-dimensional finite element model of a tumor-bearing human lower leg was constructed and was "attached" mathematically to the whole body thermal model of man described in previous studies by the authors. The central as well as local thermoregulatory feedback control mechanisms which determine blood perfusion to the various tissues and rate of evaporation by sweating were input into the limb model. In addition, the temperature of the arterial blood which feeds into the most proximal section of the lower leg was computed by the whole body thermal model. The variations in the shape of the tissues which comprise the limb were obtained from computerized tomography scans. Axial variations in the energy deposition patterns along the length of the limb exposed to a miniannular phased array (MAPA) applicator were also input into this model of limb heating. Results indicate that proper positioning of the limb relative to the MAPA is a significant factor in determining the effectiveness of the treatment. A patient-specific hyperthermia protocol can be designed using this coupled electromagnetic and thermal model.

  10. Optimal management of reconfigurable manufacturing system modeling with Petri nets developed three-dimensional - RPD3D

    NASA Astrophysics Data System (ADS)

    Teodor, F.; Marinescu, V.; Epureanu, A.

    2016-11-01

    Modeling of reconfigurable manufacturing systems would have done using existing Petri net types, but the complexity and dynamics of the new manufacturing system, mainly data reconfiguration feature, required looking for a more compact representation with many variables that to model as accurately not only the normal operation of the production system but can capture and model and reconfiguration process. Thus, it was necessary to create a new class of Petri nets, called RPD3D (Developed Petri nets with three dimensional) showing the name of both lineage (new class derived from Petri nets developed, created in 2000 by Prof. Dr. Ing Vasile Marinescu in his doctoral thesis) [1], but the most important of the new features defining (transformation from one 2D model into a 3D model).The idea was to introduce the classical model of a Petri third dimension to be able to overlay multiple levels (layers) formed in 2D or 3D Petri nets that interact with each other (receiving or giving commands to enable or disable the various modules together simulating the operation of reconfigurable manufacturing systems). The aim is to present a new type of Petri nets called RPD3D - Developed Petri three-dimensional model used for optimal control and simulation of reconfigurable manufacturing systems manufacture of products such systems.

  11. 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.

  12. A three-dimensional picture of the delayed-detonation model of type Ia supernovae

    NASA Astrophysics Data System (ADS)

    Bravo, E.; García-Senz, D.

    2008-02-01

    Aims:Deflagration models poorly explain the observed diversity of SNIa. Current multidimensional simulations of SNIa predict a significant amount of, so far unobserved, carbon and oxygen moving at low velocities. It has been proposed that these drawbacks can be resolved if there is a sudden jump to a detonation (delayed detonation), but these kinds of models have been explored mainly in one dimension. Here we present new three-dimensional delayed detonation models in which the deflagraton-to-detonation transition (DDT) takes place in conditions like those favored by one-dimensional models. Methods: We have used a smoothed-particle-hydrodynamics code adapted to follow all the dynamical phases of the explosion, with algorithms devised to handle subsonic as well as supersonic combustion fronts. The starting point was a centrally ignited C-O white dwarf of 1.38 {M}⊙. When the average density on the flame surface reached 2-3×107 g cm-3 a detonation was launched. Results: The detonation wave processed more than 0.3 M⊙ of carbon and oxygen, emptying the central regions of the ejecta of unburned fuel and raising its kinetic energy close to the fiducial 1051 erg expected from a healthy type Ia supernova. The final amount of 56Ni synthesized also was in the correct range. However, the mass of carbon and oxygen ejected is still too high. Conclusions: The three-dimensional delayed detonation models explored here show an improvement over pure deflagration models, but they still fail to coincide with basic observational constraints. However, there are many aspects of the model that are still poorly known (geometry of flame ignition, mechanism of DDT, properties of detonation waves traversing a mixture of fuel and ashes). Therefore, it will be worth pursuing its exploration to see if a good SNIa model based on the three-dimensional delayed detonation scenario can be obtained.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. A three-dimensional coupled-mode model for the acoustic field in a two-dimensional waveguide with perfectly reflecting boundaries

    NASA Astrophysics Data System (ADS)

    Luo, Wen-Yu; Yu, Xiao-Lin; Yang, Xue-Feng; Zhang, Ze-Zhong; Zhang, Ren-He

    2016-12-01

    This paper presents a three-dimensional (3D) coupled-mode model using the direct-global-matrix technique as well as Fourier synthesis. This model is a full wave, two-way three-dimensional model, and is therefore capable of providing accurate acoustic field solutions. Because the problem of sound propagation excited by a point source in an ideal wedge with perfectly reflecting boundaries is one of a few three-dimensional problems with analytical solutions, the ideal wedge problem is chosen in this work to validate the presented three-dimensional model. Numerical results show that the field results by analytical solutions and those by the presented model are in excellent agreement, indicating that the presented model can serve as a benchmark model for three-dimensional sound propagation problems involving a planar two-dimensional geometry as well as a point source. Project supported by the National Natural Science Foundation of China (Grant Nos. 11125420, 11434012, and 41561144006) and the Knowledge Innovation Program of the Chinese Academy of Sciences.

  18. [Three-dimensional morphological modeling and visualization of wheat root system].

    PubMed

    Tan, Feng; Tang, Liang; Hu, Jun-Cheng; Jiang, Hai-Yan; Cao, Wei-Xing; Zhu, Yan

    2011-01-01

    Crop three-dimensional (3D) morphological modeling and visualization is an important part of digital plant study. This paper aimed to develop a 3D morphological model of wheat root system based on the parameters of wheat root morphological features, and to realize the visualization of wheat root growth. According to the framework of visualization technology for wheat root growth, a 3D visualization model of wheat root axis, including root axis growth model, branch geometric model, and root axis curve model, was developed firstly. Then, by integrating root topology, the corresponding pixel was determined, and the whole wheat root system was three-dimensionally re-constructed by using the morphological feature parameters in the root morphological model. Finally, based on the platform of OpenGL, and by integrating the technologies of texture mapping, lighting rendering, and collision detection, the 3D visualization of wheat root growth was realized. The 3D output of wheat root system from the model was vivid, which could realize the 3D root system visualization of different wheat cultivars under different water regimes and nitrogen application rates. This study could lay a technical foundation for further development of an integral visualization system of wheat plant.

  19. 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.

  20. 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

  1. Spin transport in the frustrated anisotropic three-dimensional XY model

    NASA Astrophysics Data System (ADS)

    Lima, L. S.

    2016-12-01

    We use the SU(3) Schwinger's boson theory to study the spin transport in the frustrated anisotropic three-dimensional XY model at T=0 with single ion anisotropy. We have investigated the behavior of the spin conductivity for this model that presents exchange interactions J1, J2 and J ‧ . We study the spin transport in the Bose-Einstein regime where we have that the tz bosons are condensed i.e. = < tz†> = t . Our results show a metallic spin transport for ω > 0 and a superconductor spin transport in the limit of DC conductivity.

  2. Smarr formula for BTZ black holes in general three-dimensional gravity models

    NASA Astrophysics Data System (ADS)

    Liang, Chao; Gong, Li; Zhang, Baocheng

    2017-02-01

    Recent studies have presented the interpretation of thermodynamic enthalpy for the mass of BTZ black holes and the corresponding Smarr formula. All these are made in the background of three-dimensional (3D) general relativity. In this paper, we extend such interpretation into general 3D gravity models. It is found that the direct extension is unfeasible and some extra conditions are required to preserve both the Smarr formula and the first law of black hole thermodynamics. Thus, BTZ black hole thermodynamics enforces some constraints for general 3D gravity models, and these constraints are consistent with all previous discussions.

  3. 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.

  4. Three-dimensional fluid and electrodynamic modeling for MHD DCW channels

    NASA Astrophysics Data System (ADS)

    Liu, B. L.; Lineberry, J. T.; Schmidt, H. J.

    1983-01-01

    A three dimensional, numerical solution for modeling diagonal conducting wall (DCW) magnetohydrodynamic (MHD) generators is developed and discussed. Cross plane gasdynamic and electrodynamic profiles are computed considering coupled MHD flow and electrical phenomena. A turbulent transport model based on the mixing length theory is used to deal with wall roughness generated turbulence effects. The infinitely fine electrode segmentation formulation is applied to simplify the governing electrical equations. Calculations show the development of distorted temperature and velocity profiles under influence of magnetohydrodynamic interaction. Since both sidewall and electrode wall boundary losses are treated, the results furnish a realistic representation of MHD generator behavior.

  5. 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.

  6. Development of a three-dimensional unit cell to model the micromechanical response of a collagen-based extracellular matrix.

    PubMed

    Susilo, Monica E; Roeder, Blayne A; Voytik-Harbin, Sherry L; Kokini, Klod; Nauman, Eric A

    2010-04-01

    The three-dimensional microstructure and mechanical properties of the collagen fibrils within the extracellular matrix (ECM) is now being recognized as a primary factor in regulating cell proliferation and differentiation. Therefore, an appreciation of the mechanical aspects by which a cell interacts with its ECM is required for the development of engineered tissues. Ultimately, using these interactions to design tissue equivalents requires mathematical models with three-dimensional architecture. In this study, a three-dimensional model of a collagen fibril matrix undergoing uniaxial tensile stress was developed by making use of cellular solids. A structure consisting of thin struts was chosen to represent the arrangement of collagen fibrils within an engineered ECM. To account for the large deformation of tissues, the collagen fibrils were modeled as hyperelastic neo-Hookean or Mooney-Rivlin materials. The use of cellular solids allowed the fibril properties to be related to the ECM properties in closed form, which, in turn, allowed the estimation of fibril properties using ECM experimental data. A set of previously obtained experimental data consisting of simultaneous measures of the fibril microstructure and mechanical tests was used to evaluate the model's capability to estimate collagen fibril mechanical property when given tissue-scale data and to predict the tissue-scale mechanical properties when given estimated fibril stiffness. The fibril tangent modulus was found to be 1.26 + or - 0.70 and 1.62 + or - 0.88 MPa when the fibril was modeled as neo-Hookean and Mooney-Rivlin material, respectively. There was no statistical significance of the estimated fibril tangent modulus among the different groups. Sensitivity analysis showed that the fibril mechanical properties and volume fraction were the two input parameters which required accurate values. While the volume fraction was easily obtained from the initial image of the gel, the fibril mechanical properties

  7. Subduction-induced delamination and its surface expressions - three-dimensional numerical modelling

    NASA Astrophysics Data System (ADS)

    Ueda, Kosuke; Gerya, Taras; Willett, Sean

    2015-04-01

    Delamination during the long-term evolution of convergent plate boundaries has been interpreted as root cause for lithospheric mantle heterogeneities, and has been linked to surface observations in different stages of subduction-collision-lithospheric thinning systems. Amongst others, it has been invoked for the Apeninnes, Rhodope, and Pontides, for thinned or removed lithosphere in the Aegean and western Mediterranean, and for extensive topographic anomalies such as the Colorado or Hikurangi plateaus. With the onset of collision, in order to balance mass and to achieve either further plate convergence, subduction, or foundering of subcontinental lithospheric mantle, there is an increasing need for a mechanism to separate relatively buoyant and less buoyant material. In independent geodynamic modelling studies carried out in 2D, delamination (sensu strictu) along a horizon of minimal rheological strength has been demonstrated to satisfy this requirement. Recent work has also shown that delamination marks a gradual transition of mobile topography from tectonically dominated to mantle dominated topography over long time scales. While first order features of major observables, such as topography, and imaged lithospheric mantle thickness, can generally be reproduced in a variety of models, there is an unsatisfactory lack of uniqueness in pin-pointing the underlying mode of lithospheric mantle removal occurring at depth. In addition, strong curvatures in many orogenic systems (e.g., Western Alps, Apennines, or Carpathians) indicate that their crustal and sub-crustal evolution are intrinsically three-dimensional. To test how spatially confined delamination contributes to three-dimensional evolution, the complex arcuate curvature of resulting orogenic systems, and to the developing topography pattern, new three-dimensional models are presented. Based on recent methodological developments, and findings in 2-D delamination modelling and 3-D modelling of subduction

  8. 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

  9. Three-Dimensional Potential-Field Source-Surface Modeling of the Evolution of Coronal Structures

    NASA Astrophysics Data System (ADS)

    Wallace, Rosa; Dikpati, Mausumi; de Toma, Giuliana; Burkepile, Joan

    2017-01-01

    White-light images of the solar corona indicate that, during each solar cycle, the global structure of the corona evolves as a function of cycle phase. Building a three-dimensional potential-field source-surface model of the corona, we investigate how the longitude-dependence of coronal structure varies during solar minimum. Using white-light images of the corona from the Mauna Loa Solar Observatory (MLSO) as guidance, we derive the global three-dimensional corona from our model-output as a function of Carrington rotation, focusing on the most recent three solar minima in 1986, 1996, and 2008. Longitude-dependent coronal structures seen in white-light images are reproduced by a linear combination of spherical harmonics combined with a radial boundary condition at the source-surface, taken at 2.5 solar radii. The coefficients of spherical harmonics up to the fifth degree, as well as their phase, are deduced by comparing model-output with MLSO observations. We find that (i) during typical solar minima (such as 1986, 1996), although the axial dipole dominates, small, time-varying multipole contributions are present when analyzed over a few rotations. In addition, we find that (ii) the unusual minimum in 2008 is multipole-dominated in contrast to the solar minimum corona in 1986 and 1996. (iii) The signature of a quadrupole contribution in the 1996 corona and the further increase of multipole components in the 2008 corona indicate that the departure from dipole at minimum originated during 1996. Further analysis of the present corona will likely indicate that the next solar minimum will be non-dipolar in nature. Our estimates of the variation of multipole contributions as a function of time can be used to constrain models of the three-dimensional solar dynamo.

  10. Phase separation and bistability in a three-dimensional model for protein domain formation at biomembranes

    NASA Astrophysics Data System (ADS)

    Alonso, Sergio; Bär, Markus

    2010-12-01

    Proteins in living cells interact with membranes. They may bind to or unbind from the membrane to the cytosol depending on the lipid composition of the membrane and their interaction with cytosolic enzymes. Moreover, proteins can accumulate at the membrane and assemble in spatial domains. Here, a simple model of protein cycling at biomembranes is studied, when the total number of proteins is conserved. Specifically, we consider the spatio-temporal dynamics of MARCKS proteins and their interactions with enzymes facilitating translocation from and rebinding to the membrane. The model exhibits two qualitatively different mechanisms of protein domain formation: phase separation related to a long-wave instability of a membrane state with homogeneous protein coverage and stable coexistence of two states with different homogeneous protein coverage in bistable media. We evaluate the impact of the cytosolic volume on the occurrence of protein pattern formation by simulations in a three-dimensional model. We show that the explicit treatment of the volume in the model leads to an effective rescaling of the reaction rates. For a simplified model of protein cycling, we can derive analytical expressions for the rescaling coefficients and verify them by direct simulations with the complete three-dimensional model.

  11. 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

  12. Three-dimensional light-tissue interaction models for bioluminescence tomography

    NASA Astrophysics Data System (ADS)

    Côté, D.; Allard, M.; Henkelman, R. M.; Vitkin, I. A.

    2005-09-01

    Many diagnostic and therapeutic approaches in medical physics today take advantage of the unique properties of light and its interaction with tissues. Because light scatters in tissue, our ability to develop these techniques depends critically on our knowledge of the distribution of light in tissue. Solutions to the diffusion equation can provide such information, but often lack the flexibility required for more general problems that involve, for instance, inhomogeneous optical properties, light polarization, arbitrary three-dimensional geometries, or arbitrary scattering. Monte Carlo techniques, which statistically sample the light distribution in tissue, offer a better alternative to analytical models. First, we discuss our implementation of a validated three-dimensional polarization-sensitive Monte Carlo algorithm and demonstrate its generality with respect to the geometry and scattering models it can treat. Second, we apply our model to bioluminescence tomography. After appropriate genetic modifications to cell lines, bioluminescence can be used as an indicator of cell activity, and is often used to study tumour growth and treatment in animal models. However, the amount of light escaping the animal is strongly dependent on the position and size of the tumour. Using forward models and structural data from magnetic resonance imaging, we show how the models can help to determine the location and size of tumour made of bioluminescent cancer cells in the brain of a mouse.

  13. Numerical simulation on hydromechanical coupling in porous media adopting three-dimensional pore-scale model.

    PubMed

    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.

  14. Three-dimensional numerical modelling of water quality in Dahuofang Reservoir in China

    NASA Astrophysics Data System (ADS)

    Wang, JinHua; Shen, YongMing; Zhen, Hong; Feng, Yu; Wang, ZaiXing; Yang, Xu

    2011-07-01

    A three-dimensional eutrophication model was applied to assist the management of Dahuofang Reservoir in China. Transport processes were obtained from the three-dimensional, finite volume hydrodynamic model. The hydrodynamic model was verified for a one-year time period in 2006. Our simulation reproduced intra-annual variation of stratification. The simulated variation of vertical thermal structures also matched observations. The water quality model included 8 state variables, including dissolved oxygen, phytoplankton as carbon, carbonaceous biochemical oxygen demand, ammonium nitrogen, nitrate and nitrite nitrogen, ortho-phosphorus, organic nitrogen, and organic phosphorus. Sensitivity of the parameters has been analyzed to decide which process would affect the water quality in the simulation. The water quality verification suggested the model successfully computed the temporal cycles and spatial distributions of key water quality components. The comparison between water quality components before and after the first phase of the water conveyance project suggests that the project has a slight effect on the reservoir ecosystem. The model could be used as a tool to guide physico-biological engineering design or management strategies for Dahuofang Reservoir.

  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. A three-dimensional multiscale model of intergranular hydrogen-assisted cracking

    NASA Astrophysics Data System (ADS)

    Rimoli, J. J.; Ortiz, M.

    2010-07-01

    We present a three-dimensional model of intergranular hydrogen-embrittlement (HE) that accounts for: (i) the degradation of grain-boundary strength that arises from hydrogen coverage; (ii) grain-boundary diffusion of hydrogen; and (iii) a continuum model of plastic deformation that explicitly resolves the three-dimensional polycrystalline structure of the material. The polycrystalline structure of the specimen along the crack propagation path is resolved explicitly by the computational mesh. The texture of the polycrystal is assumed to be random and the grains are elastically anisotropic and deform plastically by crystallographic slip. We use the impurity-dependent cohesive model in order to account for the embrittling of grain boundaries due to hydrogen coverage. We have carried out three-dimensional finite-element calculations of crack-growth initiation and propagation in AISI 4340 steel double-cantilever specimens in contact with an aggressive environment and compared the predicted initiation times and crack-growth curves with the experimental data. The calculated crack-growth curves exhibit a number of qualitative features that are in keeping with observation, including: an incubation time followed by a well-defined crack-growth initiation transition for sufficiently large loading; the existence of a threshold intensity factor K Iscc below which there is no crack propagation; a subsequent steeply rising part of the curve known as stage I; a plateau, or stage II, characterized by a load-insensitive crack-growth rate; and a limiting stress-intensity factor K Ic , or toughness, at which pure mechanical failure occurs. The calculated dependence of the crack-growth initiation time on applied stress-intensity factor exhibits power-law behavior and the corresponding characteristic exponents are in the ball-park of experimental observation. The stage-II calculated crack-growth rates are in good overall agreement with experimental measurements.

  17. 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.

  18. Three-dimensional finite element modeling of a magnet array spinning above a conductor

    SciTech Connect

    Lorimer, W.L.; Lieu, D.K.; Hull, J.R.; Mulcahy, T.M.; Rossing, T.D.

    1993-12-31

    Drag forces due to eddy currents induced by the relative motion of a conductor and a magnetic field occur in many practical devices: motors, brakes, magnetic bearings, and magnetically levitated vehicles. Recently, finite element codes have included solvers for 3-D eddy current geometries and have the potential to be very useful in the design and analysis of these devices. In this paper, numerical results from three-dimensional modeling of a magnet array spinning above a conductor are compared to experimental results in order to assess the capabilities of these codes.

  19. 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.

  20. Three-dimensional model of x-ray induced microchannel plate output

    SciTech Connect

    Harding, E. C.; Drake, R. P.

    2006-10-15

    Microchannel plates are an important component in a type of imaging diagnostic known as an x-ray framing camera, used in x-ray radiography of high-energy-density physics experiments. A microchannel plate is responsible for detecting x rays and then converting them into amplified bursts of electrons, which are then imaged onto a phosphor-coated fiber optic screen. We present the preliminary development of a three-dimensional model of a single microchannel plate channel in attempt to simulate the pulse height distribution of the microchannel plate electron output. Using a novel technique, initial simulations are compared with experimental data from an ungated x-ray framing camera.

  1. 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.

  2. Relations among fault behavior, subsurface geology, and three-dimensional velocity models

    USGS Publications Warehouse

    Michael, A.J.; Eberhart-Phillips, D.

    1991-01-01

    The development of three-dimensional P-wave velocity models for the regions surrounding five large earthquakes in California has lead to the recognition of relations among fault behavior and the material properties of the rocks that contact the fault at seismogenic depths; regions of high moment release appear to correlate with high seismic velocities whereas rupture initiation or termination may be associated with lower seismic velocities. These relations point toward a physical understanding of why faults are divided into segments that can fail independently, an understanding that could improve our ability to predict earthquakes and strong ground motion.

  3. Relations among fault behavior, subsurface geology, and three-dimensional velocity models.

    PubMed

    Michael, A J; Eberhart-Phillips, D

    1991-08-09

    The development of three-dimensional P-wave velocity models for the regions surrounding five large earthquakes in California has lead to the recognition of relations among fault behavior and the material properties of the rocks that contact the fault at seismogenic depths; regions of high moment release appear to correlate with high seismic velocities whereas rupture initiation or termination may be associated with lower seismic velocities. These relations point toward a physical understanding of why faults are divided into segments that can fail independently, an understanding that could improve our ability to predict earthquakes and strong ground motion.

  4. Dendritic sidebranching in the three-dimensional symmetric model in the presence of noise

    NASA Technical Reports Server (NTRS)

    Langer, J. S.

    1987-01-01

    The time-dependent behavior of sidebranching deformations in the three-dimensional symmetric model of dendritic solidification is studied within a WKB approximation. Localized wave packets generated by pulses in the neighborhood of the tip are found to grow in amplitude and to spread and stretch as they move down the sides of the dendrite. This behavior is shown to imply that noise in the solidifying medium is selectively amplified in such a way as to produce a fluctuating train of sidebranches in qualitative agreement with experimental observations. A rough estimate indicates that purely thermal noise is probably not quite strong enough to fit the data.

  5. Modelling tidal current energy extraction in large area using a three-dimensional estuary model

    NASA Astrophysics Data System (ADS)

    Chen, Yaling; Lin, Binliang; Lin, Jie

    2014-11-01

    This paper presents a three-dimensional modelling study for simulating tidal current energy extraction in large areas, with a momentum sink term being added into the momentum equations. Due to the limits of computational capacity, the grid size of the numerical model is generally much larger than the turbine rotor diameter. Two models, i.e. a local grid refinement model and a coarse grid model, are employed and an idealized estuary is set up. The local grid refinement model is constructed to simulate the power generation of an isolated turbine and its impacts on hydrodynamics. The model is then used to determine the deployment of turbine farm and quantify a combined thrust coefficient for multiple turbines located in a grid element of coarse grid model. The model results indicate that the performance of power extraction is affected by array deployment, with more power generation from outer rows than inner rows due to velocity deficit influence of upstream turbines. Model results also demonstrate that the large-scale turbine farm has significant effects on the hydrodynamics. The tidal currents are attenuated within the turbine swept area, and both upstream and downstream of the array. While the currents are accelerated above and below turbines, which is contributed to speeding up the wake mixing process behind the arrays. The water levels are heightened in both low and high water levels as the turbine array spanning the full width of estuary. The magnitude of water level change is found to increase with the array expansion, especially at the low water level.

  6. Critical behavior of the three-dimensional Ising model with anisotropic bond randomness at the ferromagnetic-paramagnetic transition line.

    PubMed

    Papakonstantinou, T; Malakis, A

    2013-01-01

    We study the ±J three-dimensional (3D) Ising model with a spatially uniaxial anisotropic bond randomness on the simple cubic lattice. The ±J random exchange is applied on the xy planes, whereas, in the z direction, only a ferromagnetic exchange is used. After sketching the phase diagram and comparing it with the corresponding isotropic case, the system is studied at the ferromagnetic-paramagnetic transition line using parallel tempering and a convenient concentration of antiferromagnetic bonds (p(z)=0;p(xy)=0.176). The numerical data clearly point out a second-order ferromagnetic-paramagnetic phase transition belonging in the same universality class with the 3D random Ising model. The smooth finite-size behavior of the effective exponents, describing the peaks of the logarithmic derivatives of the order parameter, provides an accurate estimate of the critical exponent 1/ν=1.463(3), and a collapse analysis of magnetization data gives an estimate of β/ν=0.516(7). These results are in agreement with previous papers and, in particular, with those of the isotropic ±J three-dimensional Ising model at the ferromagnetic-paramagnetic transition line, indicating the irrelevance of the introduced anisotropy.

  7. Critical behavior of the three-dimensional Ising model with anisotropic bond randomness at the ferromagnetic-paramagnetic transition line

    NASA Astrophysics Data System (ADS)

    Papakonstantinou, T.; Malakis, A.

    2013-01-01

    We study the ±J three-dimensional (3D) Ising model with a spatially uniaxial anisotropic bond randomness on the simple cubic lattice. The ±J random exchange is applied on the xy planes, whereas, in the z direction, only a ferromagnetic exchange is used. After sketching the phase diagram and comparing it with the corresponding isotropic case, the system is studied at the ferromagnetic-paramagnetic transition line using parallel tempering and a convenient concentration of antiferromagnetic bonds (pz=0;pxy=0.176). The numerical data clearly point out a second-order ferromagnetic-paramagnetic phase transition belonging in the same universality class with the 3D random Ising model. The smooth finite-size behavior of the effective exponents, describing the peaks of the logarithmic derivatives of the order parameter, provides an accurate estimate of the critical exponent 1/ν=1.463(3), and a collapse analysis of magnetization data gives an estimate of β/ν=0.516(7). These results are in agreement with previous papers and, in particular, with those of the isotropic ±J three-dimensional Ising model at the ferromagnetic-paramagnetic transition line, indicating the irrelevance of the introduced anisotropy.

  8. A three-dimensional high Mach number asymmetric magnetopause model from global MHD simulation

    NASA Astrophysics Data System (ADS)

    Liu, Z.-Q.; Lu, J. Y.; Wang, C.; Kabin, K.; Zhao, J. S.; Wang, M.; Han, J. P.; Wang, J. Y.; Zhao, M. X.

    2015-07-01

    The numerical results from a physics-based global magnetohydrodynamic (MHD) model are used to examine the effect of the interplanetary magnetic field (IMF), solar wind dynamic pressure, and dipole tilt angle on the size and shape of the magnetopause. The subsolar magnetopause is identified using the plasma velocity and density, the cusps are identified using the thermal pressure, and the whole shape of the magnetopause is determined with the three-dimensional streamlines traced through the simulation domain. The magnetopause surface obtained from the simulations is fitted with a three-dimensional surface function controlled by ten configuration parameters, which provide a description of the subsolar magnetopause, the cusp geometry, the flaring angle, the azimuthal asymmetry, the north-south asymmetry, and the twisting angle of the magnetopause. Effects of the IMF, solar wind dynamic pressure, and dipole tilt angle on the configuration parameters are analyzed and fitted by relatively simple functions. It is found that the solar wind dynamic pressure mainly affects the magnetopause size; the IMF mainly controls the magnetopause flaring angle, azimuthal asymmetry, and twisting angle; and the dipole tilt angle mainly affects the magnetopause north-south asymmetry and the cusp geometry. The model is validated by comparing with available empirical models and observational results, and it is demonstrated that the new model can describe the magnetopause for typical solar wind conditions.

  9. Role of Topological Defects in the Phase Transition of the Three-Dimensional Heisenberg Model.

    NASA Astrophysics Data System (ADS)

    Lau, Manhot

    The role of topological point defects (hedgehogs) in the phase transition of the classical Heisenberg model in three dimensions is investigated by using Monte Carlo simulations. Simulations of the behavior of the defects near the phase transition show that the number density of defects increases sharply and defect pairs with separations comparable to the sample size begin to appear as the temperature is increased through the transition temperature. In simulations in a restricted ensemble in which spin configurations containing defects are not allowed, the system appears to remain ordered at all temperatures. Simulations in which the spin-spin interaction is set equal to zero and the number density of defects is controlled by varying a 'chemical potential' term indicate that the system is ordered if the number density of defect pairs is sufficiently small. These results show that topological defects play a crucial role in the three-dimensional Heisenberg transition in the sense that configurations containing defect pairs are necessary for the transition from the ferromagnetic to paramagnetic phase to occur. Such a conclusion is also consistent with a Renormalization Group study of the O(n) model, which suggests that topological defects should be explicitly taken into account for a correct description of the critical behavior in models including the three-dimensional Heisenberg model.

  10. Three-dimensional finite element modelling of muscle forces during mastication.

    PubMed

    Röhrle, Oliver; Pullan, Andrew J

    2007-01-01

    This paper presents a three-dimensional finite element model of human mastication. Specifically, an anatomically realistic model of the masseter muscles and associated bones is used to investigate the dynamics of chewing. A motion capture system is used to track the jaw motion of a subject chewing standard foods. The three-dimensional nonlinear deformation of the masseter muscles are calculated via the finite element method, using the jaw motion data as boundary conditions. Motion-driven muscle activation patterns and a transversely isotropic material law, defined in a muscle-fibre coordinate system, are used in the calculations. Time-force relationships are presented and analysed with respect to different tasks during mastication, e.g. opening, closing, and biting, and are also compared to a more traditional one-dimensional model. The results strongly suggest that, due to the complex arrangement of muscle force directions, modelling skeletal muscles as conventional one-dimensional lines of action might introduce a significant source of error.

  11. 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.

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

    PubMed Central

    Farahani, Mehrdad H.; Zhang, Zhaoyan

    2016-01-01

    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

  13. 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.

  14. 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.

  15. 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

  16. Three-dimensional pseudospectral modelling of cardiac propagation in an inhomogeneous anisotropic tissue.

    PubMed

    Ng, K T; Yan, R

    2003-11-01

    Various investigators have used the monodomain model to study cardiac propagation behaviour. In many cases, the governing non-linear parabolic equation is solved using the finite-difference method. An adequate discretisation of cardiac tissue with realistic dimensions, however, often leads to a large model size that is computationally demanding. Recently, it has been demonstrated, for a two-dimensional homogeneous monodomain, that the Chebyshev pseudospectral method can offer higher computational efficiency than the finite-difference technique. Here, an extension of the pseudospectral approach to a three-dimensional inhomogeneous case with fibre rotation is presented. The unknown transmembrane potential is expanded in terms of Chebyshev polynomial trial functions, and the monodomain equation is enforced at the Gauss-Lobatto node points. The forward Euler technique is used to advance the solution in time. Numerical results are presented that demonstrate that the Chebyshev pseudospectral method offered an even larger improvement in computational performance over the finite-difference method in the three-dimensional case. Specifically, the pseudospectral method allowed the number of nodes to be reduced by approximately 85 times, while the same solution accuracy was maintained. Depending on the model size, simulations were performed with approximately 18-41 times less memory and approximately 99-169 times less CPU time.

  17. Markov random field modeling for three-dimensional reconstruction of the left ventricle in cardiac angiography

    PubMed Central

    Medina, Rubén; Garreau, Mireille; Toro, Javier; Le Breton, Hervé; Coatrieux, Jean-Louis; Jugo, Diego

    2006-01-01

    This paper reports on a method for left ventricle three-dimensional reconstruction from two orthogonal ventriculograms. The proposed algorithm is voxel-based and takes into account the conical projection geometry associated with the biplane image acquisition equipment. The reconstruction process starts with an initial ellipsoidal approximation derived from the input ventriculograms. This model is subsequently deformed in such a way as to match the input projections. To this end, the object is modeled as a three-dimensional Markov-Gibbs random field, and an energy function is defined so that it includes one term that models the projections compatibility and another one that includes the space–time regularity constraints. The performance of this reconstruction method is evaluated by considering the reconstruction of mathematically synthesized phantoms and two 3-D binary databases from two orthogonal synthesized projections. The method is also tested using real biplane ventriculograms. In this case, the performance of the reconstruction is expressed in terms of the projection error, which attains values between 9.50% and 11.78 % for two biplane sequences including a total of 55 images. PMID:16895001

  18. 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.

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

    SciTech Connect

    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 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. Finally, its scope and ability to capture spatio-temporal variations of potential and lithium distribution is demonstrated on a prototypical three-dimensional electrode problem.

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

    DOE PAGES

    Allu, S.; Kalnaus, S.; Simunovic, 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

  1. Critical aspects of three-dimensional anisotropic spin-glass models

    NASA Astrophysics Data System (ADS)

    Papakonstantinou, Thodoris; Fytas, Nikolaos G.; Malakis, Anastasios; Lelidis, Ioannis

    2015-04-01

    We study the three-dimensional ± J Ising model with a longitudinal anisotropic bond randomness on the simple cubic lattice. The random exchange interaction is applied only in the z direction, whereas in the other two directions, xy-planes, we consider ferromagnetic exchange. By implementing an effective parallel tempering scheme, we outline the phase diagram of the model and compare it to the corresponding isotropic one. We present a detailed finite-size scaling analysis of the ferromagnetic-paramagnetic and spin glass-paramagnetic transition lines, and we also discuss the ferromagnetic-spin glass transition regime. We conclude that the present model shares the same universality classes with the isotropic model, but at the symmetric point has a considerably higher transition temperature from the spin-glass state to the paramagnetic phase. Our data for the ferromagnetic-spin glass transition line support a forward behavior in contrast to the reentrant behavior of the corresponding isotropic model.

  2. 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.

  3. Three-dimensional hydrological and thermal property models of Yucca Mountain, Nevada

    SciTech Connect

    Rautman, C.A.; McKenna, S.A.

    1997-11-01

    This report describes the creation of three-dimensional numerical models of selected rock-matrix properties for the region of the potential high-level nuclear waste repository site at Yucca Mountain, which is located in southern Nevada. The models have been generated for a majority of the unsaturated and shallow saturated zone within an area referred to within the Yucca Mountain Site Characterization project as the site area. They comprise a number of material properties of importance both to detailed process-level modeling activities and to more summary-style performance assessment modeling. The material properties within these models are both spatially variable (heterogeneous) and spatially correlated, as the rocks are understood from data obtained from site-characterization drill holes widely scattered across the site area.

  4. FRiED: A Novel Three-dimensional Model of Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Isavnin, A.

    2016-12-01

    We present a novel three-dimensional (3D) model of coronal mass ejections (CMEs) that unifies all key evolutionary aspects of CMEs and encapsulates their 3D magnetic field configuration. This fully analytic model is capable of reproducing the global geometrical shape of a CME with all major deformations taken into account, i.e., deflection, rotation, expansion, “pancaking,” front flattening, and rotational skew. Encapsulation of 3D magnetic structure allows the model to reproduce in-situ measurements of magnetic field for trajectories of spacecraft-CME encounters of any degree of complexity. As such, the model can be used single-handedly for the consistent analysis of both remote and in-situ observations of CMEs at any heliocentric distance. We demonstrate the latter by successfully applying the model for the analysis of two CMEs.

  5. A three-dimensional chemical transport model of the stratosphere: Midlatitude results

    NASA Astrophysics Data System (ADS)

    KamińSki, Jacek W.; McConnell, John C.; Boville, Byron A.

    1996-12-01

    A prototype robust three-dimensional global chemical transport model (CTM) has been developed in order to facilitate a realistic simulation of stratospheric chemistry and dynamics. The current application is for a 100-day run from August 10 to November 17 using the average (ensemble) of 10 dynamical runs (realizations) of the CCMl. The CTM results are compared with observations and two-dimensional model results. A comparison of the midlatitude model results with satellite observations, stratospheric and mesospheric sounder (SAMS) and Halogen Occultation Experiment (HALOE), showed that the model can simulate relatively well, at least on the timescale of the simulation, the distribution and formation of long-lived species (N2O, CH4, and H20). The distribution of short-lived species was compared with some satellite measurements, limb infrared monitor of the stratosphere (LIMS) and Stratospheric Aerosol and Gas Experiment (SAGE II), and two-dimensional model results, and was found to be consistent.

  6. Three-dimensional analysis of time varying tuft behavior by its successive geometric shape modelling

    NASA Astrophysics Data System (ADS)

    Doi, Junta; Miyake, Tetsuo

    A tuft in the air flow was observed by three CCD video cameras which were installed in the directions nearly perpendicular to each other. In this procedure, a tufted woolen yarn of the diameter of about 1 mm and of the length of 35 mm was attached on the top of a thin post pin. The principle of this shape modeling is based on the intersection of multiple viewing cones. This intersected zone results in a polyhedron when the digital image is used. It becomes a good approximation of the original shape when it is convex. This polyhedron is described with spatially fixed coordinates, so that not only its spatial shape, but also the position, direction, deformation, or fluttering at the every moment can be estimated. From this modeling, the effect of rigidity due to adhesives near the fixed end and a few millimeters of three-dimensional displacement at the free end are observed. This method is capable to serve for measurement and analysis of a single tuft characteristics, depending on its material, kind of fluid, or flow range, and has the possibility of quantitative analysis of three-dimensional unsteady flow visualization.

  7. 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.

  8. Implementation of Localized Ensemble Assimilation for a Three-Dimensional Radiation Belt Model (Invited)

    NASA Astrophysics Data System (ADS)

    Godinez, H. C.; Chen, Y.; Kellerman, A. C.; Subbotin, D.; Shprits, Y.

    2013-12-01

    Earth's outer radiation belt is very dynamic and energetic electrons therein undergo constant changes due to acceleration, loss, and trans- port processes. In this work we improve the accuracy of simulated electron phase space density (PSD) of the Versatile Electron Radiation Belt (VERB) code, a three-dimensional radiation belt model, by implementing the localized ensemble transform Kalman filter (LETKF) assimilation method. Assimilation methods based on Kalman filtering have been successfully applied to one-dimensional radial diffusion radiation belt models, where it has been shown to greatly improve the model estimation of electron phase space density (PSD). This work expands upon previous research by implementing the LETKF method to assimilate observed electron density into VERB, a three-dimensional radiation belt model. In particular, the LETKF will perform the assimilation locally, where the size of the local region is defined by the diffusion of electrons in the model. This will enable the optimal assimilation of data throughout the model consistently with the flow of electrons. Two sets of assimilation experiments are presented. The first is an identical-twin experiment, where artificial data is generated from the same model, with the purpose of verifying the assimilation method. In the second set of experiments, real PSD observational data from missions such as CRRES and/or the Van Allen Probes are assimilated into VERB. The results show that data assimilation significantly improves the accuracy of the VERB model by efficiently including the available observations at the appropriate pitch angles, energy levels, and L-shell regions throughout the model.

  9. 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.

  10. 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.

  11. Three-dimensional multiscale modeling of dendritic spacing selection during Al-Si directional solidification

    DOE PAGES

    Tourret, Damien; Clarke, Amy J.; Imhoff, Seth D.; ...

    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. Exactly solvable models of spin liquids with spinons, and of three-dimensional topological paramagnets

    NASA Astrophysics Data System (ADS)

    Ben-Zion, Daniel; Das, Diptarka; McGreevy, John

    2016-04-01

    We develop a scheme to make exactly solvable gauge theories whose electric flux lines host (1+1)-dimensional topological phases. We use this exact "decorated-string-net" framework to construct several classes of interesting models. In particular, we construct an exactly solvable model of a quantum spin liquid whose (gapped) elementary excitations form doublets under an internal symmetry, and hence may be regarded as spin-carrying spinons. The model may be formulated, and is solvable, in any number of dimensions on any bipartite graph. Another example, in any dimension, has Z2 topological order and anyons which are Kramers' doublets of time-reversal symmetry. Further, we make exactly solvable models of three-dimensional topological paramagnets.

  13. Three-dimensional thermo-fluid and electrochemical modeling of anode-supported planar solid oxide fuel cell

    NASA Astrophysics Data System (ADS)

    Qu, Zuopeng; Aravind, P. V.; Dekker, N. J. J.; Janssen, A. H. H.; Woudstra, N.; Verkooijen, A. H. M.

    This paper presents a three-dimensional model of an anode-supported planar solid oxide fuel cell with corrugated bipolar plates serving as gas channels and current collector above the active area of the cell. Conservation equations of mass, momentum, energy and species are solved incorporating the electrochemical reactions. Heat transfer due to conduction, convection and radiation is included. An empirical equation for cell resistance with measured values for different parameters is used for the calculations. Distribution of temperature and gas concentrations in the PEN (positive electrode/electrolyte/negative electrode) structure and gas channels are investigated. Variation of current density over the cell is studied. Furthermore, the effect of radiation on the temperature distribution is studied and discussed. Modeling results show that the relatively uniform current density is achieved at given conditions for the proposed design and the inclusion of thermal radiation is required for accurate prediction of temperature field in the single cell unit.

  14. Mapping three-dimensional geological features from remotely-sensed images and digital elevation models

    NASA Astrophysics Data System (ADS)

    Morris, Kevin Peter

    thinning and extraction) and manual interpretation techniques are used to identify a set of 'geological primitives' (linear or arc features representing lithological boundaries) within these data. Inclusion of the DEM data provides the three-dimensional co-ordinates of these primitives enabling a least-squares fit to be employed to calculate dip and strike values, based, initially, on the assumption of a simple, linearly dipping structural model. A very large number of scene 'primitives' is identified using these procedures, only some of which have geological significance. Knowledge-based rules are therefore used to identify the relevant. For example, rules are developed to identify lake edges, forest boundaries, forest tracks, rock-vegetation boundaries, and areas of geomorphological interest. Confidence in the geological significance of some of the geological primitives is increased where they are found independently in both the DEM and remotely sensed data. The dip and strike values derived in this way are compared to information taken from the published geological map for this area, as well as measurements taken in the field. Many results are shown to correspond closely to those taken from the map and in the field, with an error of < 1°. These data and rules are incorporated into an expert system which, initially, produces a simple model of the geological structure. The system also provides a graphical user interface for manual control and interpretation, where necessary. Although the system currently only allows a relatively simple structural model (linearly dipping with faulting), in the future it will be possible to extend the system to model more complex features, such as anticlines, synclines, thrusts, nappes, and igneous intrusions.

  15. 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.

  16. Three-dimensional multispecies nonlinear tumor growth–I. Model and numerical method

    PubMed Central

    Wise, S.M.; Lowengrub, J.S.; Frieboes, H.B.; Cristini, V.

    2012-01-01

    This is the first paper in a two-part series in which we develop, analyze and simulate a diffuse interface continuum model of multispecies tumor growth and tumor-induced angiogenesis in two and three dimensions. Three dimensional simulations of nonlinear tumor growth and neovascularization using this diffuse interface model were recently presented in Frieboes et al. (2007), but that paper did not describe the details of the model or the numerical algorithm. This is done here. In this diffuse interface approach, sharp interfaces are replaced by narrow transition layers that arise due to differential adhesive forces among the cell-species. Accordingly, a continuum model of adhesion is introduced. The model is thermodynamically consistent, is related to recently developed mixture models, and thus is capable of providing a detailed description of tumor progression. The model is well-posed and consists of fourth-order nonlinear advection-reaction-diffusion equations (of Cahn-Hilliard-type) for the cell-species coupled with reaction-diffusion equations for the substrate components. We demonstrate analytically and numerically that when the diffuse interface thickness tends to zero, the system reduces to a classical sharp interface model. Using a new fully adaptive, nonlinear multigrid/finite difference method the system is simulated efficiently. In this first paper, we present simulations of unstable avascular tumor growth in two and three dimensions and demonstrate that our techniques now make large-scale three dimensional simulations of tumors with complex morphologies computationally feasible. In Part II of this study, we will investigate multispecies tumor invasion, tumor-induced angiogenesis and focus on the morphological instabilities that may underlie invasive phenotypes. PMID:18485374

  17. Physical modeling of tsunamis generated by three-dimensional deformable granular landslides

    NASA Astrophysics Data System (ADS)

    Mohammed, Fahad; Fritz, Hermann M.

    2012-11-01

    Tsunamis generated by deformable granular landslides are physically modeled in a three-dimensional tsunami wave basin based on the generalized Froude similarity. The dynamic landslide impact characteristics were controlled by means of a novel pneumatic landslide generator. The wave amplitudes, periods, and wavelengths are related to the landslide parameters at impact with the landslide Froude number being a dominant parameter. Between 1 and 15% of the landslide kinetic energy at impact is converted into the wave train energy. The wave amplitudes decay in radial and angular directions from the landslide axis. The first wave crest mostly travels with speeds close to the theoretical approximation of the solitary wave speed. The measured tsunami wave profiles were either of the nonlinear oscillatory or nonlinear transition type depending primarily on the landslide Froude number and relative slide thickness at impact. The generated waves range from shallow to deep water depth regimes, with the majority being in the intermediate water depth regime. Wave characteristics are compared with other two- and three-dimensional landslide tsunami studies and the results are discussed.

  18. 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

  19. Damaging effects of gliadin on three-dimensional cell culture model

    PubMed Central

    Dolfini, Ersilia; Elli, Luca; Roncoroni, Leda; Costa, Barbara; Colleoni, Maria Pia; Lorusso, Vito; Ramponi, Simona; Braidotti, Paola; Ferrero, Stefano; Falini, Maria Letizia; Bardella, Maria Teresa

    2005-01-01

    AIM: To evaluate the effects of gliadin on the oxidative environment in the “ in vivo-like ”model of a three-dimensional cell culture system. METHODS: LoVo cell line (intestinal adenocarcinoma) multicellular spheroids were treated with digested gliadin (with albumin used as a control). Spheroid volumes, cell viability and morphology, lactate dehydrogenase (LDH) release, content of reduced glutathione (GSH) and activity of GSH-related enzymes were examined. The data were statistically analyzed using the Student’s t-test (P<0.05). was considered statistically significant. RESULTS: Gliadin reduced cell viability (from 20% to 60%) and led to morphological alterations characterized by apoptotic findings and cytoskeletal injuries. LDH activity increased. The content of GSH reduced (-20% vs controls), and activity of GSH-related enzymes was significantly inhibited. CONCLUSION: Gliadin treatment induces an imbalance in the antioxidative mechanism of cells cultured by the three-dimensional technique. This alteration may explain the cell damage directly caused by gliadin and the subsequent morphological abnormalities. PMID:16273608

  20. 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

  1. Model calculations for three-dimensional heat conduction in a real tooth

    NASA Astrophysics Data System (ADS)

    Foth, Hans-Jochen; Luke, Manfred

    2003-06-01

    To generate the three-dimensional grid net for a real tooth, an extracted tooth was grinded in steps of some millimetres from the top to the root. After each grinding step the displayed cross section was documented by photography showing clearly all transition lines between enamel, dentin and the pulp. The photographic reprints were used to determine the x-y-z-coordinates of selected points to represent the transition lines. In a fairly large-scale procedure these points were combined to a three dimensional net. FEM calculations were carried out to solve the heat equation numerically for the boundary condition that an IR laser pulse hits the surface for laser ablation. Since all the information of the various types of tissue is included in this model, the results give a huge variety of information. For example: the outer shell of enamel could be displayed exclusively to show its inner surface and which temperature distribution as well as mechanical stress got build up there.

  2. An analysis of three dimensional diffusion in a representative arterial wall mass transport model.

    PubMed

    Denny, William J; O'Connell, Barry M; Milroy, John; Walsh, Michael T

    2013-05-01

    The development and use of drug eluting stents has brought about significant improvements in reducing in-stent restenosis, however, their long term presence in the artery is still under examination due to restenosis reoccurring. Current studies focus mainly on stent design, coatings and deployment techniques but few studies address the issue of the physics of three dimensional mass transport in the artery wall. There is a dearth of adequate validated numerical mass transport models that simulate the physics of diffusion dominated drug transport in the artery wall whilst under compression. A novel experimental setup used in a previous study was adapted and an expansion of that research was carried out to validate the physics of three dimensional diffusive mass transport into a compressed porous media. This study developed a more sensitive method for measuring the concentration of the species of interest. It revalidated mass transport in the radial direction and presented results which highlight the need for an evaluation of the governing equation for transient diffusive mass transport in a porous media, in its current form, to be carried out.

  3. 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.

  4. 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.

  5. Three-fluid, Three-dimensional Magnetohydrodynamic Solar Wind Model with Eddy Viscosity and Turbulent Resistivity

    NASA Astrophysics Data System (ADS)

    Usmanov, Arcadi V.; Goldstein, Melvyn L.; Matthaeus, William H.

    2014-06-01

    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

  6. Three-dimensional reservoir geological modeling of the Cano Limon Field, Colombia

    SciTech Connect

    Budding, M.C.; Paardekam, A.H.M. ); Flint, S.S. ); Dubrule, O.R.F. )

    1990-05-01

    The Cano Limon field is located in Colombia, and had a STOIP of 2 bbl. A three-dimensional geological reservoir model has been constructed with the computer program MONARCH, on the basis of data from 24 wells, The model includes the high net/gross fluvio-deltaic M1 reservoir, and the overlying C5 reservoir, which consists of an undeveloped low net/gross coastal plain sequence. The modeling project was restricted to an area of 9 x 3 km. The Cano Limon model is represented by a matrix of 1.75 million volume elements (voxels) each measuring 50 x 50 m horizontally and 0.6 m vertically. At each voxel the model indicates whether shale or sand is present. If sand is present, MONARCH differentiates between three types of genetic sand body types: channel, mouth bars, and crevasse splays. Correlatable sands are mapped using a deterministic approach and the lateral extent of noncorrelatable sand bodies is derived using statistical distributions of width-thickness ratios. These distributions are directly derived from the information given by Cano Limon well data about the degree of correlativity of the sand bodies. MONARCH combines structural information, as derived from seismic, with information about sand body orientation as provided by dipmeter data oriented cores, and seismic amplitude maps. In the case of Cano Limon which is produced by a strong natural water drive with an unfavorable mobility ratio of 11, this level of integration helps provide reliable guidelines regarding the development of the field. Although the upper C5 reservoir is yet undeveloped, the 24 production wells can hypothetically be completed in the MONARCH models. Calculations indicate that 60% of the total oil-bearing reservoir volume in the C5 reservoir is connected to 23 of the 24 wells. MONARCH allows the geologist to input as much geological knowledge as is appropriate in the three-dimensional reservoir model.

  7. 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

  8. A three-dimensional multi-agent-based model for the evolution of Chagas' disease.

    PubMed

    Galvão, Viviane; Miranda, José Garcia Vivas

    2010-06-01

    A better understanding of Chagas' disease is important because the knowledge about the progression and the participation of the different types of cells in this disease are still lacking. To clarify this system, the kinetics of inflammatory cells and parasite nests was shown in an experiment. Using this experimental data, we have developed a three-dimensional multi-agent-based computational model for the evolution of Chagas' disease. Our model includes five different types of agents: inflammatory cell, fibrosis, cardiomyocyte, fibroblast, and Trypanosoma cruzi. Fibrosis is fixed and the other types of agents can move through the empty space. They move randomly by using the Moore neighborhood. This model reproduces the acute and chronic phases of Chagas' disease and the volume occupied by all different types of cells in the cardiac tissue.

  9. A hybrid model for three-dimensional simulations of sprouting angiogenesis.

    PubMed

    Milde, Florian; Bergdorf, Michael; Koumoutsakos, Petros

    2008-10-01

    Recent advances in cancer research have identified critical angiogenic signaling pathways and the influence of the extracellular matrix on endothelial cell migration. These findings provide us with insight into the process of angiogenesis that can facilitate the development of effective computational models of sprouting angiogenesis. In this work, we present the first three-dimensional model of sprouting angiogenesis that considers explicitly the effect of the extracellular matrix and of the soluble as well as matrix-bound growth factors on capillary growth. The computational model relies on a hybrid particle-mesh representation of the blood vessels and it introduces an implicit representation of the vasculature that can accommodate detailed descriptions of nutrient transport. Extensive parametric studies reveal the role of the extracellular matrix structure and the distribution of the different vascular endothelial growth factors isoforms on the dynamics and the morphology of the generated vascular networks.

  10. A Hybrid Model for Three-Dimensional Simulations of Sprouting Angiogenesis

    PubMed Central

    Milde, Florian; Bergdorf, Michael; Koumoutsakos, Petros

    2008-01-01

    Recent advances in cancer research have identified critical angiogenic signaling pathways and the influence of the extracellular matrix on endothelial cell migration. These findings provide us with insight into the process of angiogenesis that can facilitate the development of effective computational models of sprouting angiogenesis. In this work, we present the first three-dimensional model of sprouting angiogenesis that considers explicitly the effect of the extracellular matrix and of the soluble as well as matrix-bound growth factors on capillary growth. The computational model relies on a hybrid particle-mesh representation of the blood vessels and it introduces an implicit representation of the vasculature that can accommodate detailed descriptions of nutrient transport. Extensive parametric studies reveal the role of the extracellular matrix structure and the distribution of the different vascular endothelial growth factors isoforms on the dynamics and the morphology of the generated vascular networks. PMID:18586846

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Three-dimensional Monte Carlo model of the coffee-ring effect in evaporating colloidal droplets

    NASA Astrophysics Data System (ADS)

    Crivoi, A.; Duan, Fei

    2014-03-01

    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.

  17. 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.

  18. Abundance analysis of the halo giant HD 122563 with three-dimensional model stellar atmospheres

    NASA Astrophysics Data System (ADS)

    Collet, R.; Nordlund, Å.; Asplund, M.; Hayek, W.; Trampedach, R.

    We present a preliminary local thermodynamic equilibrium (LTE) abundance analysis of the template halo red giant HD122563 based on a realistic, three-dimensional (3D), time-dependent, hydrodynamical model atmosphere of the very metal-poor star. We compare the results of the 3D analysis with the abundances derived by means of a standard LTE analysis based on a classical, 1D, hydrostatic model atmosphere of the star. Due to the different upper photospheric temperature stratifications predicted by 1D and 3D models, we find large, negative, 3D-1D LTE abundance differences for low-excitation OH and Fe I lines. We also find trends with lower excitation potential in the derived Fe LTE abundances from Fe I lines, in both the 1D and 3D analyses. Such trends may be attributed to the neglected departures from LTE in the spectral line formation calculations.

  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. An unstructured grid, three-dimensional model based on the shallow water equations

    NASA Astrophysics Data System (ADS)

    Casulli, Vincenzo; Walters, Roy A.

    2000-02-01

    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

  1. 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.

  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. 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.

  4. 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.

  5. 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.

  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. Twisted gauge theories in three-dimensional Walker-Wang models

    NASA Astrophysics Data System (ADS)

    Wang, Zitao; Chen, Xie

    2017-03-01

    Three-dimensional gauge theories with a discrete gauge group can emerge from spin models as a gapped topological phase with fractional point excitations (gauge charge) and loop excitations (gauge flux). It is known that 3D gauge theories can be "twisted," in the sense that the gauge flux loops can have nontrivial braiding statistics among themselves and such twisted gauge theories are realized in models discovered by Dijkgraaf and Witten. A different framework to systematically construct three-dimensional topological phases was proposed by Walker and Wang and a series of examples have been studied. Can the Walker-Wang construction be used to realize the topological order in twisted gauge theories? This is not immediately clear because the Walker-Wang construction is based on a loop condensation picture while the Dijkgraaf-Witten theory is based on a membrane condensation picture. In this paper, we show that the answer to this question is Yes, by presenting an explicit construction of the Walker-Wang models which realize both the twisted and untwisted gauge theories with gauge group Z2×Z2 . We identify the topological order of the models by performing modular transformations on the ground-state wave functions and show that the modular matrices exactly match those for the Z2×Z2 gauge theories. By relating the Walker-Wang construction to the Dijkgraaf-Witten construction, our result opens up a way to study twisted gauge theories with fermonic charges, and correspondingly strongly interacting fermionic symmetry protected topological phases and their surface states, through exactly solvable models.

  8. Near-field diffraction simulation on three-dimensional mask model with off-axis illumination

    NASA Astrophysics Data System (ADS)

    Cheng, Lin; Cao, Peng-fei; Liu, Jia; Zhang, Xiao-ping

    2009-05-01

    In 45nm technology node and beyond with hyper NA and Off-axis Illumination(OAI) lithography simulation, mask topography effect is not ignorable, for calculating near-field distribution based on scalar diffraction theory is insufficient on accuracy. Real three-dimensional (3D) simulation is required for precise evaluation of printing performance and the accuracy of 3D mask model on simulation is a key issue, especially for the mask with contact holes, corners or island patterns, even for 3D defect detection. In this paper, a general 3D mask model on simulation is presented and its near-field diffraction distributions can be described by the thickness of mask, the oblique incident angle, azimuth angle and polarization. Example of simulations are implemented on 3D mask with contact hole without or with optical proximity correction (OPC) assistant patterns, we get the same results as those from rigorous electromagnetic field simulation (REMFS).

  9. Measuring and modeling the thermal conductivities of three-dimensionally woven fabric composites

    NASA Astrophysics Data System (ADS)

    Schuster, J.; Heider, D.; Sharp, K.; Glowania, M.

    2009-03-01

    The effect of a three-dimensional fiber reinforcement on the out-of-plane thermal conductivity of composite materials is investigated. Composite preforms with different fibers in the thickness direction were fabricated. After in fusion by using a vacuum-assisted resin transfer molding process, their through-thickness thermal conductivities were evaluated. The measured thermal conductivities showed a significant increase compared with those of a typical laminated composite. Although the through-thickness thermal conductivity of the samples increased with through-thickness fiber volume fraction, its values did not match those predicted by the simple rule of mixtures. By using finite-element models to better under stand the behavior of the composite material, improvements in an existing analytical model were performed to predict the effective thermal conductivity as a function of material properties and in-contact thermal properties of the composite.

  10. Finite element analysis of a three-dimensional open-celled model for trabecular bone.

    PubMed

    Beaupre, G S; Hayes, W C

    1985-08-01

    Based on a regular array of cubic unit cells, each containing a body-centered spherical void, we created an idealized three-dimensional model for both subchondral trabecular bone and a class of porous foams. By considering only face-to-face stacking of unit cells, the inherent symmetry was such that, except at the surface, the displacements and stresses within any one unit cell were representative of the entire porous structure. Using prescribed displacements the model was loaded in both uniaxial compressive strain and uniaxial shear strain. Based on the response to these loads, we found the tensor of elastic constants for an equivalent homogeneous elastic solid with cubic symmetry. We then compared the predicted modulus with our experimental values for bovine trabecular bone and literature values for an open-celled latex rubber foam.

  11. Non-Newtonian bile flow in elastic cystic duct: one- and three-dimensional modeling.

    PubMed

    Li, W G; Luo, X Y; Chin, S B; Hill, N A; Johnson, A G; Bird, N C

    2008-11-01

    Bile flow is thought to play an essential role in the pathophysiological genesis of cholelithiasis (gallstone formation) and in gallbladder pain. In this paper, we extend our previous study of the human biliary system (Li et al., 2007, J. Biomech. Eng., 129:164-173) to include two important factors: the non-Newtonian properties of bile, and elastic deformation of the cystic duct. A one-dimensional (1D) model is analyzed and compared with three-dimensional (3D) fluid-structure interaction simulations. It is found that non-Newtonian bile raises resistance to the flow of bile, which can be augmented significantly by the elastic deformation (collapse) of the cystic duct. We also show that the 1D model predicts the pressure drop of the cystic duct flow well for all cases considered (Newtonian or non-Newtonian flow, rigid or elastic ducts), when compared with the full 3D simulations.

  12. 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)

  13. 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.

  14. Static and dynamic structure factors in three-dimensional randomly diluted Ising models.

    PubMed

    Calabrese, Pasquale; Pelissetto, Andrea; Vicari, Ettore

    2008-02-01

    We consider the three-dimensional randomly diluted Ising model and study the critical behavior of the static and dynamic spin-spin correlation functions (static and dynamic structure factors) at the paramagnetic-ferromagnetic transition in the high-temperature phase. We consider a purely relaxational dynamics without conservation laws, the so-called model A. We present Monte Carlo simulations and perturbative field-theoretical calculations. While the critical behavior of the static structure factor is quite similar to that occurring in pure Ising systems, the dynamic structure factor shows a substantially different critical behavior. In particular, the dynamic correlation function shows a large-time decay rate which is momentum independent. This effect is not related to the presence of the Griffiths tail, which is expected to be irrelevant in the critical limit, but rather to the breaking of translational invariance, which occurs for any sample and which, at the critical point, is not recovered even after the disorder average.

  15. 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.

  16. Linear surface roughness growth and flow smoothening in a three-dimensional biofilm model

    NASA Astrophysics Data System (ADS)

    Head, D. A.

    2013-09-01

    The sessile microbial communities known as biofilms exhibit varying architectures as environmental factors are varied, which for immersed biofilms includes the shear rate of the surrounding flow. Here we modify an established agent-based biofilm model to include affine flow and employ it to analyze the growth of surface roughness of single-species, three-dimensional biofilms. We find linear growth laws for surface geometry in both horizontal and vertical directions and measure the thickness of the active surface layer, which is shown to anticorrelate with roughness. Flow is shown to monotonically reduce surface roughness without affecting the thickness of the active layer. We argue that the rapid roughening is due to nonlocal surface interactions mediated by the nutrient field, which are curtailed when advection competes with diffusion. We further argue the need for simplified models to elucidate the underlying mechanisms coupling flow to growth.

  17. 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.

  18. 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.

  19. Lumped versus distributed thermoregulatory control: results from a three-dimensional dynamic model.

    PubMed

    Werner, J; Buse, M; Foegen, A

    1989-01-01

    In this study we use a three-dimensional model of the human thermal system, the spatial grid of which is 0.5 ... 1.0 cm. The model is based on well-known physical heat-transfer equations, and all parameters of the passive system have definite physical values. According to the number of substantially different areas and organs, 54 spatially different values are attributed to each physical parameter. Compatibility of simulation and experiment was achieved solely on the basis of physical considerations and physiological basic data. The equations were solved using a modification of the alternating direction implicit method. On the basis of this complex description of the passive system close to reality, various lumped and distributed parameter control equations were tested for control of metabolic heat production, blood flow and sweat production. The simplest control equations delivering results on closed-loop control compatible with experimental evidence were determined. It was concluded that it is essential to take into account the spatial distribution of heat production, blood flow and sweat production, and that at least for control of shivering, distributed controller gains different from the pattern of distribution of muscle tissue are required. For sweat production this is not so obvious, so that for simulation of sweating control after homogeneous heat load a lumped parameter control may be justified. Based on these conclusions three-dimensional temperature profiles for cold and heat load and the dynamics for changes of the environmental conditions were computed. In view of the exact simulation of the passive system and the compatibility with experimentally attainable variables there is good evidence that those values extrapolated by the simulation are adequately determined. The model may be used both for further analysis of the real thermoregulatory mechanisms and for special applications in environmental and clinical health care.

  20. Comparison between iteration schemes for three-dimensional coordinate-transformed saturated-unsaturated flow model

    NASA Astrophysics Data System (ADS)

    An, Hyunuk; Ichikawa, Yutaka; Tachikawa, Yasuto; Shiiba, Michiharu

    2012-11-01

    SummaryThree different iteration methods for a three-dimensional coordinate-transformed saturated-unsaturated flow model are compared in this study. The Picard and Newton iteration methods are the common approaches for solving Richards' equation. The Picard method is simple to implement and cost-efficient (on an individual iteration basis). However it converges slower than the Newton method. On the other hand, although the Newton method converges faster, it is more complex to implement and consumes more CPU resources per iteration than the Picard method. The comparison of the two methods in finite-element model (FEM) for saturated-unsaturated flow has been well evaluated in previous studies. However, two iteration methods might exhibit different behavior in the coordinate-transformed finite-difference model (FDM). In addition, the Newton-Krylov method could be a suitable alternative for the coordinate-transformed FDM because it requires the evaluation of a 19-point stencil matrix. The formation of a 19-point stencil is quite a complex and laborious procedure. Instead, the Newton-Krylov method calculates the matrix-vector product, which can be easily approximated by calculating the differences of the original nonlinear function. In this respect, the Newton-Krylov method might be the most appropriate iteration method for coordinate-transformed FDM. However, this method involves the additional cost of taking an approximation at each Krylov iteration in the Newton-Krylov method. In this paper, we evaluated the efficiency and robustness of three iteration methods—the Picard, Newton, and Newton-Krylov methods—for simulating saturated-unsaturated flow through porous media using a three-dimensional coordinate-transformed FDM.

  1. 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…

  2. Three-dimensional modeling of capsule implosions in OMEGA tetrahedral hohlraums

    SciTech Connect

    Schnittman, J. D.; Craxton, R. S.

    2000-07-01

    Tetrahedral hohlraums have been proposed as a means for achieving the highly uniform implosions needed for ignition with inertial confinement fusion (ICF) [J. D. Schnittman and R. S. Craxton, Phys. Plasmas 3, 3786 (1996)]. Recent experiments on the OMEGA laser system have achieved good drive uniformity consistent with theoretical predictions [J. M. Wallace et al., Phys. Rev. Lett. 82, 3807 (1999)]. To better understand these experiments and future investigations of high-convergence ICF implosions, the three-dimensional (3-D) view-factor code BUTTERCUP has been expanded to model the time-dependent radiation transport in the hohlraum and the hydrodynamic implosion of the capsule. Additionally, a 3-D postprocessor has been written to simulate x-ray images of the imploded core. Despite BUTTERCUP's relative simplicity, its predictions for radiation drive temperatures, fusion yields, and core deformation show close agreement with experiment. (c) 2000 American Institute of Physics.

  3. Three-dimensional modeling of capsule implosions in OMEGA tetrahedral hohlraums

    NASA Astrophysics Data System (ADS)

    Schnittman, J. D.; Craxton, R. S.

    2000-07-01

    Tetrahedral hohlraums have been proposed as a means for achieving the highly uniform implosions needed for ignition with inertial confinement fusion (ICF) [J. D. Schnittman and R. S. Craxton, Phys. Plasmas 3, 3786 (1996)]. Recent experiments on the OMEGA laser system have achieved good drive uniformity consistent with theoretical predictions [J. M. Wallace et al., Phys. Rev. Lett. 82, 3807 (1999)]. To better understand these experiments and future investigations of high-convergence ICF implosions, the three-dimensional (3-D) view-factor code BUTTERCUP has been expanded to model the time-dependent radiation transport in the hohlraum and the hydrodynamic implosion of the capsule. Additionally, a 3-D postprocessor has been written to simulate x-ray images of the imploded core. Despite BUTTERCUP's relative simplicity, its predictions for radiation drive temperatures, fusion yields, and core deformation show close agreement with experiment.

  4. Three-Dimensional Modelling inside a Differential Pressure Laminar Flow Bioreactor Filled with Porous Media

    PubMed Central

    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. PMID:26301245

  5. Correlation of experimental data and three-dimensional finite element modeling of a spinning magnet array

    SciTech Connect

    Lorimer, W.L.; Lieu, D.K.; Hull, J.R.; Mulcahy, T.M.; Rossing, T.D.

    1994-09-01

    Drag forces due to eddy currents induced by the relative motion of a conductor and a magnetic field occur in many practical devices: motors, brakes, magnetic bearings, and magnetically levitated vehicles. Here, a magnet array was spun above an aluminum disk, and the drag torque was measured for various speeds and gap sizes. Drag torques calculated using a three-dimensional finite element program were consistent with measured values. The finite element model was also used to determine the effects of the polarity and position of magnets in the source array. The peak torque was shown to occur when magnets are located at a radius equal to 70% of the disk radius. A magnet array with alternate magnets reversed was shown to produce more than twice the drag of an array comprised of parallel magnets. An approximation for fields under the magnet centers was obtained using a two-dimensional analytical solution.

  6. Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach

    NASA Astrophysics Data System (ADS)

    Kovalenko, Andriy; Truong, Thanh N.

    2000-11-01

    We developed a self-consistent three-dimensional reference interaction site model integral equation theory with the molecular hypernetted chain closure (SC-3D-RISM/HNC) for studying thermochemistry of solvation of ionic solutes in a polar molecular solvent. It is free from the inconsistency in the positions of the ion-solvent site distribution peaks, peculiar to the conventional RISM/HNC approach and improves the predictions for the solvation thermodynamics. The SC-3D-RISM treatment can be readily generalized to the case of finite ionic concentrations, including the consistent dielectric corrections to provide a consistent description of the dielectric properties of ion-molecular solution. The proposed theory is tested for hydration of the Na+ and Cl- ions in ambient water at infinite dilution. An improved agreement of the ion hydration structure and thermodynamics with molecular simulation results is found as compared to the conventional RISM/HNC treatment.

  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. 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.

  9. 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.

  10. Integrated three-dimensional models for noninvasive monitoring and valorization of the Morgantina silver treasure (Sicily)

    NASA Astrophysics Data System (ADS)

    Alberghina, Maria Francesca; Alberghina, Filippo; Allegra, Dario; Di Paola, Francesco; Maniscalco, Laura; Milazzo, Giuseppe; Milotta, Filippo L. M.; Pellegrino, Lorella; Schiavone, Salvatore; Stanco, Filippo

    2017-01-01

    The Morgantina silver treasure belonging to the Archaeological Museum of Aidone (Sicily) was involved in a three-dimensional (3-D) survey and diagnostics campaign for monitoring the collection over time in anticipation of their temporary transfer to the Metropolitan Museum of Art in New York for a period of 4 years. Using a multidisciplinary approach, a scientific and methodological protocol based on noninvasive techniques to achieve a complete and integrated knowledge of the precious items and their conservation state, as well as to increase their valorization, has been developed. All acquired data, i.e., 3-D models, ultraviolet fluorescence, x-ray images, and chemical information, will be made available, in an integrated way, within a web-oriented platform, which will present an in-progress tool to deepen existing archaeological knowledge and production technologies and to obtain referenced information of the conservation state before and after moving of the collection from its exposure site.

  11. 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.

  12. Simulation of synthetic aperture imaging ladar (SAIL) for three-dimensional target model

    NASA Astrophysics Data System (ADS)

    Yi, Ning; Wu, Zhen-Sen

    2010-11-01

    In conventional imaging laser radar, the resolution of target is constrained by the diffraction-limited, which includes the beamwidth of the laser in the target plane and the telescope's aperture. Synthetic aperture imaging Ladar (SAIL) is an imaging technique which employs aperture synthesis with coherent laser radar, the resolution is determined by the total frequency spread of the source and is independent of range, so can achieve fine resolution in long range. Ray tracing is utilized here to obtain two-dimensional scattering properties from three-dimensional geometric model of actual target, and range-doppler algorithm is used for synthetic aperture process in laser image simulation. The results show that the SAIL can support better resolution.

  13. 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.

  14. Monopole mass in the three-dimensional Georgi-Glashow model

    NASA Astrophysics Data System (ADS)

    Davis, A. C.; Hart, A.; Kibble, T. W.; Rajantie, A.

    2002-06-01

    We study the three-dimensional Georgi-Glashow model to demonstrate how magnetic monopoles can be studied fully nonperturbatively in lattice Monte Carlo simulations, without any assumptions about the smoothness of the field configurations. We examine the apparent contradiction between the conjectured analytic connection of the “broken” and “symmetric” phases, and the interpretation of the mass (i.e., the free energy) of the fully quantized ’t Hooft Polyakov monopole as an order parameter to distinguish the phases. We use Monte Carlo simulations to measure the monopole free energy and its first derivative with respect to the scalar mass. On small volumes we compare this to semiclassical predictions for the monopole. On large volumes we show that the free energy is screened to zero, signaling the formation of a confining monopole condensate. This screening does not allow the monopole mass to be interpreted as an order parameter, resolving the paradox.

  15. Modelling the dynamics of condensation and evaporation of fluids in three-dimensional slit pores

    NASA Astrophysics Data System (ADS)

    Casselman, Joshua A.; Desouza, Anish; Monson, Peter A.

    2015-05-01

    We present an application of dynamic mean field theory (DMFT) for lattice gas models of confined fluids to the case of a fluid in a three-dimensional narrow slit between two plates. We consider a process where the slit is in contact with a subcritical bulk vapour and the bulk chemical potential is changed from a dilute gas value to a value close to that of the bulk saturated vapour so that capillary condensation occurs in the pore. DMFT predicts that the nucleation process during the condensation occurs by the formation of multiple liquid bridges spanning the pore walls, starting in the corners of the slit. These bridges eventually coalesce and the condensation transition terminates through the shrinkage and disappearance of a vapour bubble. We find that the density distribution is sensitive to the dimensions of the slit, with the number of bridges increasing with the slit area.

  16. Three-Dimensional Numerical Model Considering Phase Transformation in Friction Stir Welding of Steel

    NASA Astrophysics Data System (ADS)

    Cho, Hoon-Hwe; Kim, Dong-Wan; Hong, Sung-Tae; Jeong, Yong-Ha; Lee, Keunho; Cho, Yi-Gil; Kang, Suk Hoon; Han, Heung Nam

    2015-12-01

    A three-dimensional (3D) thermo-mechanical model is developed considering the phase transformation occurring during the friction stir welding (FSW) of steel, and the simulated result is compared with both the measured temperature distribution during FSW and the microstructural changes after FSW. The austenite grain size (AGS) decreases significantly because of the frictional heat and severe plastic deformation generated during FSW, and the decreased AGS accelerates the diffusional phase transformation during FSW. The ferrite phase, one of the diffusional phases, is developed mainly in mild steel, whereas the bainite phase transformation occurs significantly in high-strength steel with large hardenability. Additionally, transformation-induced heat is observed mainly in the stir zone during FSW. The measured temperature distribution and phase fraction agree fairly well with the predicted data.

  17. Three-dimensional interferometric ISAR imaging for target scattering diagnosis and modeling.

    PubMed

    Xu, X; Narayanan, R M

    2001-01-01

    Two-dimensional (2-D) inverse synthetic aperture radar (ISAR) imaging has been widely used in target scattering diagnosis, modeling and target identification. A major shortcoming is that a 2-D ISAR image cannot provide information on the relative altitude of each scattering center on the target. In this paper, we present an interferometric inverse synthetic aperture radar (IF-ISAR) image processing technique for three-dimensional (3-D) target altitude image formation. The 2-D ISAR images are obtained from the signature data acquired as a function of frequency and azimuthal angle. A 3-D IF-ISAR altitude image can then be derived from two 2-D images reconstructed from the measurements by antennas at different altitudes. 3-D altitude image formation examples from both indoor and outdoor test range data are demonstrated on complex radar targets.

  18. 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.

  19. 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.

  20. Three-dimensional photoionization modelling of the planetary nebula NGC 3918

    NASA Astrophysics Data System (ADS)

    Ercolano, B.; Morisset, C.; Barlow, M. J.; Storey, P. J.; Liu, X.-W.

    2003-04-01

    The three-dimensional Monte Carlo photoionization code MOCASSIN has been applied to construct a realistic model of the planetary nebula NGC 3918. Three different geometric models were tried, the first being the biconical density distribution already used some years ago by Clegg et al. In this model the nebula is approximated by a biconical structure of enhanced density, embedded in a lower-density spherical region. Spindle-like density distributions were used for the other two models (models A and B). Model A used a mass distribution slightly modified from one of Mellema's hydrodynamical models that had already been adopted by Corradi et al. for their observational analysis of NGC 3918. Our spindle-like model B instead used an analytical expression to describe the shape of the inner shell of this object as consisting of an ellipsoid embedded in a sphere. The effects of the interaction of the diffuse fields coming from two adjacent regions of different densities were investigated. These are found to be non-negligible, even for the relatively uncomplicated case of a biconical geometry. We found that the ionization structure of low-ionization species near the boundaries is particularly affected. It is found that all three models provided acceptable matches to the integrated nebular optical and ultraviolet spectrum. Large discrepancies were found between all of the model predictions of infrared fine-structure line fluxes and ISO SWS measurements. This was found to be largely due to an offset of ~14 arcsec from the centre of the nebula that affected all of the ISO observations of NGC 3918. For each model, we also produced projected emission-line maps and position-velocity diagrams from synthetic long-slit spectra, which could be compared to recent HST images and ground-based long-slit echelle spectra. This comparison showed that spindle-like model B provided the best match to the observations. Although the integrated emission-line spectrum of NGC 3918 can be reproduced

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Three-Dimensional Modeling of Fluid and Heat Transport in an Accretionary Complex

    NASA Astrophysics Data System (ADS)

    Paula, C. A.; Ge, S.; Screaton, E. J.

    2001-12-01

    As sediments are scraped off of the subducting oceanic crust and accreted to the overriding plate, the rapid loading causes pore pressures in the underthrust sediments to increase. The change in pore pressure drives fluid flow and heat transport within the accretionary complex. Fluid is channeled along higher permeability faults and fractures and expelled at the seafloor. In this investigation, we examined the effects of sediment loading on fluid flow and thermal transport in the decollement at the Barbados Ridge subduction zone. Both the width and thickness of the Barbados Ridge accretionary complex increase from north to south. The presence of mud diapers south of the Tiburon Rise and an observed southward decrease in heat flow measurements indicate that the increased thickness of the southern Barbados accretionary prism affects the transport of chemicals and heat by fluids. The three-dimensional geometry and physical properties of the accretionary complex were utilized to construct a three-dimensional fluid flow/heat transport model. We calculated the pore pressure change due to a period of sediment loading and added this to steady-state pressure conditions to generate initial conditions for transient simulations. We then examined the diffusion of pore pressure and possible perturbation of the thermal regime over time due to loading of the underthrust sediments. The model results show that the sediment-loading event was sufficient to create small temperature fluctuations in the decollement zone. The magnitude of temperature fluctuation in the decollement was greatest at the deformation front but did not vary significantly from north to south of the Tiburon Rise.

  6. 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.

  7. Lifetime prediction for the subsurface crack propagation using three-dimensional dynamic FEA model

    NASA Astrophysics Data System (ADS)

    Yin, Yuan; Chen, Yun-Xia; Liu, Le

    2017-03-01

    The subsurface crack propagation is one of the major interests for gear system research. The subsurface crack propagation lifetime is the number of cycles remaining for a spall to appear, which can be obtained through either stress intensity factor or accumulated plastic strain analysis. In this paper, the heavy loads are applied to the gear system. When choosing stress intensity factor, the high compressive stress suppresses Mode I stress intensities and severely reduces Mode II stress intensities in the heavily loaded lubricated contacts. Such that, the accumulated plastic strain is selected to calculate the subsurface crack propagation lifetime from the three-dimensional FEA model through ANSYS Workbench transient analysis. The three-dimensional gear FEA dynamic model with the subsurface crack is built through dividing the gears into several small elements. The calculation of the total cycles of the elements is proposed based on the time-varying accumulated plastic strain, which then will be used to calculate the subsurface crack propagation lifetime. During this process, the demonstration from a subsurface crack to a spall can be uncovered. In addition, different sizes of the elements around the subsurface crack are compared in this paper. The influences of the frictional coefficient and external torque on the crack propagation lifetime are also discussed. The results show that the lifetime of crack propagation decreases significantly when the external load T increasing from 100 N m to 150 N m. Given from the distributions of the accumulated plastic strain, the lifetime shares no significant difference when the frictional coefficient f ranging in 0.04-0.06.

  8. 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

  9. A data-constrained three-dimensional magnetohydrodynamic simulation model for a coronal mass ejection initiation

    NASA Astrophysics Data System (ADS)

    Wu, S. T.; Zhou, Yufen; Jiang, Chaowei; Feng, Xueshang; Wu, Chin-Chun; Hu, Qiang

    2016-02-01

    In this study, we present a three-dimensional magnetohydrodynamic model based on an observed eruptive twisted flux rope (sigmoid) deduced from solar vector magnetograms. This model is a combination of our two very well tested MHD models: (i) data-driven 3-D magnetohydrodynamic (MHD) active region evolution (MHD-DARE) model for the reconstruction of the observed flux rope and (ii) 3-D MHD global coronal-heliosphere evolution (MHD-GCHE) model to track the propagation of the observed flux rope. The 6 September 2011, AR11283, event is used to test this model. First, the formation of the flux rope (sigmoid) from AR11283 is reproduced by the MHD-DARE model with input from the measured vector magnetograms given by Solar Dynamics Observatory/Helioseismic and Magnetic Imager. Second, these results are used as the initial boundary condition for our MHD-GCHE model for the initiation of a coronal mass ejection (CME) as observed. The model output indicates that the flux rope resulting from MHD-DARE produces the physical properties of a CME, and the morphology resembles the observations made by STEREO/COR-1.

  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. Investigation on a gas-liquid ejector using three-dimensional CFD model

    NASA Astrophysics Data System (ADS)

    Kang, S. H.; Song, X. G.; Park, Y. C.

    2012-11-01

    This paper is focusing on the numeral study of a gas-liquid ejector used for ballast water treatment. The gasliquid ejector is investigated through steady three-dimensional multiphase CFD analysis with commercial software ANSYS-CFX 13.0. Water as the primary fluid is driven through the driving nozzle and air is ejected into as the second gas instead of the ozone in real application. Several turbulence models such as Standard k-ɛ model, RNG k-ɛ model, SST model and k-ω model, and different mesh size and compared extensively with the experimental results to eliminate the influence of the auxiliary system, turbulence models and mesh generation. The appropriate numerical model in terms of the best combination of turbulence model and mesh size are used in the subsequent research the study the influence of the operating condition such as the driving pressure/velocity and the back pressure of the ejector on its performance. The results provide deep insight on the influence of various factors on the performance of gas-liquid ejector. And the proposed numerical model will be very helpful in the further design optimization of the gas-liquid ejectors.

  12. 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.

  13. A three-dimensional, multinutrient, and size-structured ecosystem model for the North Atlantic

    NASA Astrophysics Data System (ADS)

    Lima, Ivan D.; Doney, Scott C.

    2004-09-01

    We incorporate multinutrient and size-structured ecosystem dynamics into a three-dimensional ocean general circulation model for the North Atlantic. The model reproduces the magnitude and general spatial and temporal patterns in nutrients, chlorophyll and primary production seen in in situ (BATS, NABE, and OWSI) and satellite (SeaWiFS) data, showing substantial improvements over prior basin-scale simulations. Model skill is evaluated quantitatively against SeaWiFS data using a Taylor diagram approach. Model-data correlation R for the overall surface chlorophyll time-space distribution is ˜0.6, with comparable model and observed total variability. The agreement relative to satellite-based primary production is somewhat weaker (0.2 < R < 0.5). The simulations capture observed ecological characteristics, e.g., the dominance of picoplankton and episodic diatom blooms in the subtropics, nutrient-controlled plankton succession at higher latitudes, and associated seasonal/depth changes in new and regenerated production and particle export. In a sensitivity experiment that mimics behavior of simpler single-species models, removal of diatom silica limitation leads to major shifts in community structure and export and larger model-data errors similar to previous model studies. Model results also suggest that episodic diatom blooms at BATS may be related to interannual variations in the southward transport of nutrients, mainly SiO3, and plankton cells.

  14. Three-dimensional seasonal deformations induced by underground gas storage. Monitoring by PSI and modeling by FE

    NASA Astrophysics Data System (ADS)

    Teatini, P.; Lovison, A.; Janna, C.; Ferretti, A.

    2012-04-01

    Land subsidence and uplift due to the production/injection of fluids from/into the subsurface have been widely observed worldwide over the last decades and occur for a variety of purposes such as groundwater pumping, aquifer system recharge, gas/oil field development, enhanced oil recovery, geologic CO2 sequestration, underground gas storage and waste disposal. The need for a reliable prediction of these processes has led to a continuous improvement of the numerical tools employed in poromechanics. However, although sophisticated poro-visco-plastic 3D codes have been developed, the lack of accurate measurements of the ground surface displacements has rarely allowed an accurate calibration of the geomechanical models. Recently, advanced Persistent Scatterer Interferometry data, obtained by combining ascending and descending RADARSAT-1 images acquired from 2003 to 2008 above gas storage fields located in the sedimentary basin of the Po river plain, Italy, provide reliable measurement of seasonal vertical ups and downs as well as horizontal displacements to and from the injection/withdrawal wells. Combination of the land surface movements together with an accurate reconstruction of the subsurface geology made available by three-dimensional seismic surveys and long-time records of fluid pore pressure within the 1000-1500 m deep reservoirs has allowed for the development of an accurate 3D transversally isotropic poromechanical finite-element model which satisfactorily reproduces the seasonal deformation due to gas injection/removal. An accurate calibration of the finite element model to the interferometry data is performed by combining metamodeling techniques such as Kriging and global optimization strategies specifically designed for handling uncertain measurements. Furthermore, it is also possible to estimate the functional dependence of physically relevant quantities, e.g., the maximum vertical seasonal displacement, with respect to operational parameters (e

  15. 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

  16. Automated calibration of a three-dimensional ground water flow model

    SciTech Connect

    Baker, F.G.; Guo, X.; Zigich, D.

    1996-12-31

    A three-dimensional ground water flow model was developed and calibrated for use as a quantitative tool for the evaluation of several potential ground water remedial alternatives during the On-Post Feasibility Study for the Rocky Mountain Arsenal. The USGS MODFLOW code was implemented and calibrated for steady-state conditions over the entire model area and for transient conditions where local pumping test data were available. Strict modeling goals and calibration criteria were established before modeling was initiated and formed a basis to guide the modeling process as it proceeded. The modeling effort utilized a non-traditional optimization technique to assist in model calibration. During calibration, this practical and systematic parameter adjustment procedure was used where parameter change was tightly constrained by preset geologic and hydrogeologic conditions. Hydraulic conductivity parameter was adjusted based on frequent comparison of calculated head to observed head conditions. The driving parameter was adjusted within limits until the calibration criteria achieved predetermined calibration targets. The paper presents the calibration approach and discusses the model application for evaluation of alternatives.

  17. One-dimensional and three-dimensional models of cerebrovascular flow.

    PubMed

    Moore, S M; Moorhead, K T; Chase, J G; David, T; Fink, J

    2005-06-01

    The Circle of Willis is a ring-like structure of blood vessels found beneath the hypothalamus at the base of the brain. Its main function is to distribute oxygen-rich arterial blood to the cerebral mass. One-dimensional (1D) and three-dimensional (3D) computational fluid dynamics (CFD) models of the Circle of Willis have been created to provide a simulation tool which can potentially be used to identify at-risk cerebral arterial geometries and conditions and replicate clinical scenarios, such as occlusions in afferent arteries and absent circulus vessels. Both models capture cerebral haemodynamic autoregulation using a proportional-integral (PI) controller to modify efferent artery resistances to maintain optimal efferent flow rates for a given circle geometry and afferent blood pressure. The models can be used to identify at-risk cerebral arterial geometries and conditions prior to surgery or other clinical procedures. The 1D model is particularly relevant in this instance, with its fast solution time suitable for real-time clinical decisions. Results show the excellent correlation between models for the transient efferent flux profile. The assumption of strictly Poiseuille flow in the 1D model allows more flow through the geometrically extreme communicating arteries than the 3D model. This discrepancy was overcome by increasing the resistance to flow in the anterior communicating artery in the 1D model to better match the resistance seen in the 3D results.

  18. 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

  19. Three-dimensional Keplerian orbit-superposition models of the nucleus of M31

    NASA Astrophysics Data System (ADS)

    Brown, C. K.; Magorrian, J.

    2013-05-01

    We present three-dimensional eccentric disc models of the nucleus of M31, modelling the disc as a linear combination of thick rings of massless stars orbiting in the potential of a central black hole. Our models are non-parametric generalizations of the parametric models of Peiris and Tremaine. The models reproduce well the observed Wide Field Planetary Camera 2 photometry, the detailed line-of-sight velocity distributions from Space Telescope Spectroscopy Imaging Spectrograph observations along P1 and P2, together with the qualitative features of the OASIS kinematic maps. We confirm Peiris and Tremaine's finding that nuclear discs aligned with the larger disc of M31 are strongly ruled out. Our optimal model is inclined at 57° with respect to the line of sight of M31 and has position angle PA = θl + 90° = 55°. It has a central black hole of mass M• ≃ 1.0 × 108 M⊙, and, when viewed in three dimensions, shows a clear enhancement in the density of stars around the black hole. The distribution of orbit eccentricities in our models is similar to Peiris and Tremaine's model, but we find significantly different inclination distributions, which might provide valuable clues to the origin of the disc.

  20. Development and validation of a three-dimensional ring-based structural tyre model

    NASA Astrophysics Data System (ADS)

    Kindt, P.; Sas, P.; Desmet, W.

    2009-10-01

    This paper presents a structural model for an unloaded tyre, based on a three-dimensional flexible ring on an elastic foundation. The ring represents the belt and the elastic foundation represents the tyre sidewall. The model is valid up to 300 Hz and includes a submodel of the wheel and the air cavity. This makes the model potentially suitable for the prediction of structure-borne interior noise. Unlike most ring models, which only consider in-plane modes, the presented model also predicts the modes that involve torsion of the belt in circumferential direction. The parameterization of the model, which does not require detailed knowledge of the tyre construction, is based on the main geometrical properties of the tyre and a limited modal test. Comparison between measured and calculated responses shows that the tyre-wheel model describes the dynamic behaviour with acceptable accuracy. Since the model is physical, it can be applied to describe other operational conditions such as loading and rotation.

  1. 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.

  2. 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.

  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 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Three-dimensional FDTD Modeling of Earth-ionosphere Cavity Resonances

    NASA Astrophysics Data System (ADS)

    Yang, H.; Pasko, V. P.

    2003-12-01

    Resonance properties of the earth-ionosphere cavity were first predicted by W. O. Schumann in 1952 [Schumann, Z. Naturforsch. A, 7, 149, 1952]. Since then observations of extremely low frequency (ELF) signals in the frequency range 1-500 Hz have become a powerful tool for monitoring of global lightning activity and planetary scale variability of the lower ionosphere, as well as, in recent years, for location and remote sensing of sprites, jets and elves and associated lightning discharges [e.g., Sato et al., JASTP, 65, 607, 2003; Su et al., Nature, 423, 974, 2003; and references cited therein]. The simplicity and flexibility of finite difference time domain (FDTD) technique for finding first principles solutions of electromagnetic problems in a medium with arbitrary inhomogeneities and ever-increasing computer power make FDTD an excellent candidate to be the technique of the future in development of realistic numerical models of VLF/ELF propagation in Earth-ionosphere waveguide [Cummer, IEEE Trans. Antennas Propagat., 48, 1420, 2000], and several reports about successful application of the FDTD technique for solution of related problems have recently appeared in the literature [e.g., Thevenot et al., Ann. Telecommun., 54, 297, 1999; Cummer, 2000; Berenger, Ann. Telecommun., 57, 1059, 2002, Simpson and Taflove, IEEE Antennas Wireless Propagat. Lett., 1, 53, 2002]. In this talk we will present results from a new three-dimensional spherical FDTD model, which is designed for studies of ELF electromagnetic signals under 100 Hz in the earth-ionosphere cavity. The model accounts for a realistic latitudinal and longitudinal variation of ground conductivity (i.e., for the boundaries between oceans and continents) by employing a broadband surface impedance technique proposed in [Breggs et al., IEEE Trans. Antenna Propagat., 41, 118, 1993]. The realistic distributions of atmospheric/lower ionospheric conductivity are derived from the international reference ionosphere model

  10. 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.

  11. 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.

  12. 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.

  13. Transferability of a Three-Dimensional Air Quality Model between Two Different Sites in Complex Terrain.

    NASA Astrophysics Data System (ADS)

    Lange, Rolf

    1989-07-01

    The three-dimensional, diagnostic, particle-in-cell transport and diffusion model MATHEW/ADPIC is used to test its transferability from one site in complex terrain to another with different characteristics, under stable nighttime drainage flow conditions. The two sites were subject to extensive drainage flow tracer experiments under the multilaboratory Atmospheric Studies in Complex Terrain (ASCOT) program: the first being a valley in the Geysers geothermal region of northern California, and the second a canyon in western Colorado. The domain in each case is approximately 10 × 10 km. The 1980 Geysers model evaluation is only quoted. The 1984 Brush Creek model evaluation is described in detail.Results from comparing computed with measured concentrations from a variety of tracer releases indicate that 52% of the 4531 samples from five experiments in Brush Creek and 50% of the 831 samples from four experiments in the Geysers agreed within a factor of 5. When an angular 10° uncertainty, consistent with anemometer reliability limits in complex terrain, was allowed to be applied to the model results, model performance improved such that 78% of samples compared within a factor of 5 for Brush Creek and 77% for the Geysers. Looking at the range of other factors of concentration ratios, results indicate that the model is satisfactorily transferable without tuning it to a specific site.

  14. 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

  15. An IBM-compatible program for interactive three-dimensional gravity modeling

    NASA Astrophysics Data System (ADS)

    Broome, John

    1992-04-01

    G3D is a 3-D interactive gravity modeling program for IBM-compatible microcomputers. The program allows a model to be created interactively by defining multiple tabular bodies with horizontal tops and bottoms. The resulting anomaly is calculated using Plouff's algorithm at up to 2000 predefined random or regularly located points. In order to display the anomaly as a color image, the point data are interpolated onto a regular grid and quantized into discrete intervals. Observed and residual gravity field images also can be generated. Adjustments to the model are made using a graphics cursor to move, insert, and delete body points or whole bodies. To facilitate model changes, planview body outlines can be overlain on any of the gravity field images during editing. The model's geometry can be displayed in planview or along a user-defined vertical section. G3D is written in Microsoft® FORTRAN and utilizes the Halo-Professional® (or Halo-88®) graphics subroutine library. The program is written for use on an IBM-compatible microcomputer equipped with hard disk, numeric coprocessor, and VGA, Number Nine Revolution (Halo-88® only), or TIGA® compatible graphics cards. A mouse or digitizing tablet is recommended for cursor positioning. Program source code, a user's guide, and sample data are available as Geological Survey of Canada Open File (G3D: A Three-dimensional Gravity Modeling Program for IBM-compatible Microcomputers).

  16. A new three-dimensional magneto-viscoelastic model for isotropic magnetorheological elastomers

    NASA Astrophysics Data System (ADS)

    Agirre-Olabide, I.; Lion, A.; Elejabarrieta, M. J.

    2017-03-01

    In this work, a four-parameter fractional derivative viscoelastic model was developed to describe the dynamic shear behaviour of magnetorheological elastomers (MREs) as a function of the matrix, particle content and magnetic field. The material parameters were obtained from experimental data measured with a Physica MCR 501 rheometer from the Anton Paar Company, equipped with a magnetorheological cell. The synthetised isotropic MRE samples were based on room-temperature vulcanising silicone rubber and spherical carbonyl iron powder micro particles as fillers, and seven volumetric particle contents were studied. The influence of particle contents was included in each parameter of the four-parameter fractional derivative model. The dependency of the storage modulus as a function of an external magnetic field (magnetorheological (MR) effect) was studied, and a dipole–dipole interaction model was used. A new three-dimensional magneto-viscoelastic model was developed to couple the viscoelastic model, the particle-matrix interaction and the magneto-induced modulus model, which predicts the influence of the magnetic field and the particle content in the MR effect of isotropic MREs.

  17. A k-Omega Turbulence Model for Quasi-Three-Dimensional Turbomachinery Flows

    NASA Technical Reports Server (NTRS)

    Chima, Rodrick V.

    1995-01-01

    A two-equation k-omega turbulence model has been developed and applied to a quasi-three-dimensional viscous analysis code for blade-to-blade flows in turbomachinery. the code includes the effects of rotation, radius change, and variable stream sheet thickness. The flow equations are given and the explicit runge-Kutta solution scheme is described. the k-omega model equations are also given and the upwind implicit approximate-factorization solution scheme is described. Three cases were calculated: transitional flow over a flat plate, a transonic compressor rotor, and transonic turbine vane with heat transfer. Results were compared to theory, experimental data, and to results using the Baldwin-Lomax turbulence model. The two models compared reasonably well with the data and surprisingly well with each other. Although the k-omega model behaves well numerically and simulates effects of transition, freestream turbulence, and wall roughness, it was not decisively better than the Baldwin-Lomax model for the cases considered here.

  18. 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.

  19. 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.

  20. In vivo images of the epidural space with two- and three-dimensional optical coherence tomography in a porcine model

    PubMed Central

    Tsou, Mei-Yung

    2017-01-01

    Background No reports exist concerning in vivo optical coherence tomography visualization of the epidural space and the blood patch process in the epidural space. In this study, we produced real-time two-dimensional and reconstructed three-dimensional images of the epidural space by using optical coherence tomography in a porcine model. We also aimed to produce three-dimensional optical coherence tomography images of the dura puncture and blood patch process. Methods Two-dimensional and three-dimensional optical coherence tomography images were obtained using a swept source optical coherence tomography (SSOCT) system. Four laboratory pigs were intubated and ventilated after the induction of general anesthesia. An 18-gauge Tuohy needle was used as a tunnel for the optical coherence tomography probe to the epidural space. Two-dimensional and three-dimensional reconstruction optical coherence tomography images of the epidural space were acquired in four stages. Results In stage 1, real-time two-dimensional and reconstructed three-dimensional optical coherence tomography of the lumbar and thoracic epidural space were successfully acquired. In stage 2, the epidural catheter in the epidural space was successfully traced in the 3D optical coherence tomography images. In stage 3, water injection and lumbar puncture were successfully monitored in all study animals. In stage 4, 10 mL of fresh blood was injected into the epidural space and two-dimensional and three-dimensional optical coherence tomography images were successfully acquired. Conclusions These animal experiments suggest the potential capability of using an optical coherence tomography-based imaging needle in the directed two-dimensional and three-dimensional visualization of the epidural space. More investigations involving humans are required before optical coherence tomography can be recommended for routine use. However, three-dimensional optical coherence tomography may provide a novel, minimally invasive

  1. 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.

  2. 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

  3. Simulations of the February 1979 stratospheric sudden warming: Model comparisons and three-dimensional evolution

    NASA Technical Reports Server (NTRS)

    Manney, G. L.; Farrara, J. D.; Mechoso, C. R.

    1994-01-01

    The evolution of the stratopsheric flow during the major stratospheric sudden warming of February 1979 is studied using two primitive equation models of the stratosphere and mesosphere. The United Kingdom Meteorological Office Stratosphere-Mesosphere Model (SMM) uses log pressure as a vertical coordinate. A spectral, entropy coordinate version of the SMM (entropy coordinate model, or ECM) that has recently been developed is also used. Comparison of SMM simulations with forecasts performed using the University of California, Los Angeles general circulation model confirms the previously noted sensitivity of stratospheric forecasts to tropospheric forecasts and emphasizes the importance of adequate vertical resolution in modeling the stratosphere. The ECM simulations provide a schematic description of the three-dimensional evolution of the polar vortex and the motion of air through it. During the warming, the two cyclonic vortices tilt westward and equatorward with height. Strong upward velocities develop in the lower stratosphere on the west (cold) side of a baroclinic zone as it forms over Europe and Asia. Strong downward velocities appear in the upper stratosphere on the east (warm) side, strengthening the temperature gradients. After the peak of the warming, vertical velocities decrease, downward velocities move into the lower stratosphere, and upward velocities move into the upper stratosphere.

  4. 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.

  5. A Basic Protein Comparative Three-Dimensional Modeling Methodological Workflow Theory and Practice.

    PubMed

    Bitar, Mainá; Franco, Glória Regina

    2014-01-01

    When working with proteins and studying its properties, it is crucial to have access to the three-dimensional structure of the molecule. If experimentally solved structures are not available, comparative modeling techniques can be used to generate useful protein models to subsidize structure-based research projects. In recent years, with Bioinformatics becoming the basis for the study of protein structures, there is a crescent need for the exposure of details about the algorithms behind the softwares and servers, as well as a need for protocols to guide in silico predictive experiments. In this article, we explore different steps of the comparative modeling technique, such as template identification, sequence alignment, generation of candidate structures and quality assessment, its peculiarities and theoretical description. We then present a practical step-by-step workflow, to support the Biologist on the in silico generation of protein structures. Finally, we explore further steps on comparative modeling, presenting perspectives to the study of protein structures through Bioinformatics. We trust that this is a thorough guide for beginners that wish to work on the comparative modeling of proteins.

  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. 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.

  8. Three-dimensional ionospheric tomography reconstruction using the model function approach in Tikhonov regularization

    NASA Astrophysics Data System (ADS)

    Wang, Sicheng; Huang, Sixun; Xiang, Jie; Fang, Hanxian; Feng, Jian; Wang, Yu

    2016-12-01

    Ionospheric tomography is based on the observed slant total electron content (sTEC) along different satellite-receiver rays to reconstruct the three-dimensional electron density distributions. Due to incomplete measurements provided by the satellite-receiver geometry, it is a typical ill-posed problem, and how to overcome the ill-posedness is still a crucial content of research. In this paper, Tikhonov regularization method is used and the model function approach is applied to determine the optimal regularization parameter. This algorithm not only balances the weights between sTEC observations and background electron density field but also converges globally and rapidly. The background error covariance is given by multiplying background model variance and location-dependent spatial correlation, and the correlation model is developed by using sample statistics from an ensemble of the International Reference Ionosphere 2012 (IRI2012) model outputs. The Global Navigation Satellite System (GNSS) observations in China are used to present the reconstruction results, and measurements from two ionosondes are used to make independent validations. Both the test cases using artificial sTEC observations and actual GNSS sTEC measurements show that the regularization method can effectively improve the background model outputs.

  9. 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.

  10. Automated recovery of three-dimensional models of plant shoots from multiple color images.

    PubMed

    Pound, Michael P; French, Andrew P; Murchie, Erik H; Pridmore, Tony P

    2014-12-01

    Increased adoption of the systems approach to biological research has focused attention on the use of quantitative models of biological objects. This includes a need for realistic three-dimensional (3D) representations of plant shoots for quantification and modeling. Previous limitations in single-view or multiple-view stereo algorithms have led to a reliance on volumetric methods or expensive hardware to record plant structure. We present a fully automatic approach to image-based 3D plant reconstruction that can be achieved using a single low-cost camera. The reconstructed plants are represented as a series of small planar sections that together model the more complex architecture of the leaf surfaces. The boundary of each leaf patch is refined using the level-set method, optimizing the model based on image information, curvature constraints, and the position of neighboring surfaces. The reconstruction process makes few assumptions about the nature of the plant material being reconstructed and, as such, is applicable to a wide variety of plant species and topologies and can be extended to canopy-scale imaging. We demonstrate the effectiveness of our approach on data sets of wheat (Triticum aestivum) and rice (Oryza sativa) plants as well as a unique virtual data set that allows us to compute quantitative measures of reconstruction accuracy. The output is a 3D mesh structure that is suitable for modeling applications in a format that can be imported in the majority of 3D graphics and software packages.

  11. Spontaneous alignment of frustrated bonds in an anisotropic, three-dimensional Ising model

    NASA Astrophysics Data System (ADS)

    Jalabert, Rodolfo A.; Sachdev, Subir

    1991-07-01

    The Ising model on a three-dimensional cubic lattice with all plaquettes in the x-y frustrated plane is studied by use of a Monte Carlo technique; the exchange constants are of equal magnitude, but have varying signs. At zero temperature, the model has a finite entropy and no long-range order. The low-temperature phase is characterized by an order parameter measuring the openZ4 symmetry of lattice rotations which is invariant under Mattis gauge transformation; fluctuations lead to the alignment of frustrated bonds into columns and a fourfold degeneracy. An additional factor-of-2 degeneracy is obtained from a global spin flip. The order vanishes at a critical temperature by a transition that appears to be in the universality class of the D=3, XY model. These results are consistent with the theoretical predictions of Blankschtein et al. This Ising model is related by duality to phenomenological models of two-dimensional frustrated quantum antiferromagnets.

  12. 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.

  13. Three-dimensional modeling of ozone and particulate matter: Model improvement and evaluation

    NASA Astrophysics Data System (ADS)

    Liu, Ping

    ammonia (NH3) and sulfur dioxide (SO2), dry deposition velocity of nitric acid (HNO3), and gas-phase oxidation of SO2 by hydroxyl radical (OH)) in the final sensitivity simulation improves the overall performance of CMAQ in terms of SO42-, nitrate (NO3 -), and ammonium (NH4+). CMAQ-MADRID 2_FAST can reduce CPU time by 47% in three-dimensional simulations compared to original CMAQ-MADRID 2, with a reasonable compromise on accuracy. This reduction is not as much as that from the MADRID 2_FAST box model simulations. The likely reasons include the high computational demand of the gas-phase mechanism calculation (about 44% of total CPU time), and the relatively lower biogenic VOC emissions over most of the domain. CMAQ and CMAQ-MADRID 1 and 2 have similar performances for O3, and CMAQ-MADRID 1 and 2 give better performance for PM2.5 because of the higher predicted organic carbons (OC), though the significant OC overpredictions occur in the western U.S. that is likely due to the uncertainties in primary OC emissions in that region. CMAQ-MADRID 2_FAST is further applied for a seasonal episode (i.e., contiguous U.S., June, July, and August 2001) and the results show the reliable performance for O3 and PM2.5.

  14. 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

  15. Three-dimensional Numerical Models of Slab Edges: Implications for Mantle Upwelling and Anomalous Volcanism

    NASA Astrophysics Data System (ADS)

    Jadamec, M.; Moresi, L. N.; Durance-Sie, P. M.; Mclean, K. A.

    2013-05-01

    Adakitic volcanics associated with slab edges have been identified in numerous localities (Defant and Drummond (1990); Yogodzinski et al. (2001); Durance et al. (2012)). However, there is a range in composition as well as hypothesized petrogenetic formation for the samples worldwide designated as adakites (e.g., Yogodzinski and Kelemen (1998); Thorkelson and Breitsprecher (2005); Castillo (2012)). Three-dimensional (3D) models investigating the solid state flow in the mantle due to subduction with a slab edge predict toroidal flow around the slab edge and an associated upward component of flow that may be important for the generation of adakites (Schellart (2004); Piromallo et al. (2006); Jadamec and Billen (2010); Schellart (2010); Jadamec and Billen (2012)). However, the position of the slab edge at depth and associated location of upwelling in the mantle relative to the location of the observed anomalous volcanics on the surface have not been studied in detail. Three-dimensional high-resolution numerical models of subduction are used to investigate slab edge associated mantle upwelling and the potential links to the formation of adakites. The numerical models are geographically referenced to specific subduction zone settings and are constructed with SlabGenerator (Jadamec and Billen, 2010, 2012). The mantle convection code CitcomCU is used to solve for the viscous flow (Moresi and Solomatov, 1995; Moresi and Gurnis, 1996; Zhong, 2006). Specific slab edges settings investigated are the Antilles subduction zone in the eastern Caribbean, the Scotia subduction zone-back arc spreading system, the eastern Alaska subduction-transform system, and the eastern New Hebrides slab edge-back arc spreading system. The models suggest upwelling associated with the return flow around the slab edge can lead to decompression melting located within several hundred kilometers outward of the slab edge, and thus contribute to melting of the slab edge and the formation of adakites. In

  16. 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.

  17. 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.

  18. 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.

  19. A three-dimensional constitutive model for the stress relaxation of articular ligaments.

    PubMed

    Davis, Frances M; De Vita, Raffaella

    2014-06-01

    A new nonlinear constitutive model for the three-dimensional stress relaxation of articular ligaments is proposed. The model accounts for finite strains, anisotropy, and strain-dependent stress relaxation behavior exhibited by these ligaments. The model parameters are identified using published uniaxial stress-stretch and stress relaxation data on human medial collateral ligaments (MCLs) subjected to tensile tests in the fiber and transverse to the fiber directions (Quapp and Weiss in J Biomech Eng Trans ASME 120:757-763, 1998; Bonifasi-Lista et al. in J Orthop Res 23(1):67-76, 2005). The constitutive equation is then used to predict the nonlinear elastic and stress relaxation response of ligaments subjected to shear deformations in the fiber direction and transverse to the fiber direction, and an equibiaxial extension. A direct comparison with stress relaxation data collected by subjecting human MCLs to shear deformation in the fiber direction is presented in order to demonstrate the predictive capabilities of the model.

  20. 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.

  1. The discovery of novel auxin transport inhibitors by molecular modeling and three-dimensional pattern analysis

    NASA Astrophysics Data System (ADS)

    Bures, Mark G.; Black-Schaefer, Candace; Gardner, Gary

    1991-08-01

    Molecular modeling techniques and three-dimensional (3D) pattern analysis have been used to investigate the chemical and steric properties of compounds that inhibit transport of the plant hormone auxin. These compounds bind to a specific site on the plant plasma membrane characterized by its affinity for the herbicide N-1-naphthylphthalamic acid (NPA). A 3D model was derived from critical features of a set of ligands for the NPA receptor, a suggested binding conformation is proposed, and implications for the topographical features of the NPA receptor are discussed. This model, along with 3D structural analysis techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the criteria of the model, 77 representative molecules were evaluated for their ability to compete for the binding of [3H]NPA to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, representing chemical classes not included in the original compound set, were also found to inhibit polar auxin transport through corn coleoptile sections. Thus, this study demonstrates that 3D analysis techniques can identify active, novel ligands for biochemical target sites with concomitant physiological activity.

  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. Characterization and three-dimensional reconstruction of synthetic bone model foams.

    PubMed

    Gómez, S; Vlad, M D; López, J; Navarro, M; Fernández, E

    2013-08-01

    Sawbones© open-cell foams with different porosity grades are being used as synthetic bone-like models for in vitro mechanical and infiltration experiments. However, a comprehensive characterization of these foams is not available and there is a lack of reliable information about them. For this reason two of these foams (Refs. 1522-505 and -507) have been characterized at the micro architectural level by scanning electron microscopy, computed tomography and image data analysis. BoneJ open software and ImageJ open software were used to obtain the characteristic histomorphometric parameters and the three dimensional virtual models of the foams. The results showed that both foams, while having different macro porosities, appeared undistinguishable at the micro scale. Moreover, the micro structural features resembled those of osteoporotic rather than healthy trabecular bone. It is concluded that Sawbones© foams behave reasonably as synthetic bone-like models. Consequently, their use is recommended for in vitro comparison purposes of both mechanical and infiltration testing performed in real vertebra. Finally, the virtual models obtained, which are available under request, can favour comparisons between future self-similar in vitro experiments and computer simulations.

  4. Generation, validation, and utilization of a three-dimensional pharmacophore model for EP3 antagonists.

    PubMed

    Mishra, Rama K; Singh, Jasbir

    2010-08-23

    Studies reported here are aimed to investigate the important structural features that characterize the human EP(3) antagonists. Based on the knowledge of low-energy conformation of the endogenous ligand, the initial hit analogs were prepared. Subsequently, a ligand-based lead optimization approach using pharmacophore model generation was utilized. A 5-point pharmacophore using a training set of 19 compounds spanning the IC(50) data over 4-log order was constructed using the HypoGen module of Catalyst. Following pharmacophore customization, using a linear structure-activity regression equation, a six feature three-dimensional predictive pharmacophore model, P6, was built, which resulted in improved predictive power. The P6 model was validated using a test set of 11 compounds providing a correlation coefficient (R(2)) of 0.90 for predictive versus experimental EP(3) IC(50) values. This pharmacophore model has been expanded to include diverse chemotypes, and the predictive ability of the customized pharmacophore has been tested.

  5. Predicting crystal growth via a unified kinetic three-dimensional partition model.

    PubMed

    Anderson, Michael W; Gebbie-Rayet, James T; Hill, Adam R; Farida, Nani; Attfield, Martin P; Cubillas, Pablo; Blatov, Vladislav A; Proserpio, Davide M; Akporiaye, Duncan; Arstad, Bjørnar; Gale, Julian D

    2017-04-03

    Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails dividing the structure into 'natural tiles' or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a diverse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and l-cystine.

  6. 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.

  7. A three-dimensional laboratory steam injection model allowing in situ saturation measurements

    SciTech Connect

    Demiral, B.M.R.; Pettit, P.A.; Castanier, L.M.; Brigham, W.E.

    1992-08-01

    The CT imaging technique together with temperature and pressure measurements were used to follow the steam propagation during steam and steam foam injection experiments in a three dimensional laboratory steam injection model. The advantages and disadvantages of different geometries were examined to find out which could best represent radial and gravity override flows and also fit the dimensions of the scanning field of the CT scanner. During experiments, steam was injected continuously at a constant rate into the water saturated model and CT scans were taken at six different cross sections of the model. Pressure and temperature data were collected with time at three different levels in the model. During steam injection experiments, the saturations obtained by CT matched well with the temperature data. That is, the steam override as observed by temperature data was also clearly seen on the CT pictures. During the runs where foam was present, the saturation distributions obtained from CT pictures showed a piston like displacement. However, the temperature distributions were different depending on the type of steam foam process used. The results clearly show that the pressure/temperature data alone are not sufficient to study steam foam in the presence of non-condensible gas.

  8. 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.

  9. Predicting water age distribution in the Pearl River Estuary using a three-dimensional model

    NASA Astrophysics Data System (ADS)

    Ren, Yuheng; Lin, Binliang; Sun, Jian; Pan, Shunqi

    2014-11-01

    The age of water (AW) concept is applied to investigate the water exchange process in a large and density stratified estuary, namely the Pearl River Estuary. A three-dimensional AW model has been built based on an existing hydrodynamic and solute transport model. The model is used to determine the AW distributions inside the Pearl River Estuary under various hydrodynamic conditions. The predicted mean AW values during the dry and wet seasons are approximately 25 and 10 days, respectively. In general, lower AW values are observed in the upper layers near the water surface, while higher values are observed in the lower layers near the bed. The difference becomes more pronounced during the wet season when the river discharge is very large. The tidal influence is relatively small. The variation of tidal forcing impacts mainly on the AW fluctuation range, but it has limited impact on the tidally averaged AW value. Moreover, the AW vertical difference is enhanced during neap tides. A comparison between the predictions using barotropic and baroclinic models indicates that the density-induced circulation has a significant impact on the water exchange rate.

  10. 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.

  11. 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.

  12. 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.

  13. Anthropomorphic model observer performance in three-dimensional detection task for low-contrast computed tomography.

    PubMed

    Ba, Alexandre; Eckstein, Miguel P; Racine, Damien; Ott, Julien G; Verdun, Francis; Kobbe-Schmidt, Sabine; Bochud, François O

    2016-01-01

    X-ray medical imaging is increasingly becoming three-dimensional (3-D). The dose to the population and its management are of special concern in computed tomography (CT). Task-based methods with model observers to assess the dose-image quality trade-off are promising tools, but they still need to be validated for real volumetric images. The purpose of the present work is to evaluate anthropomorphic model observers in 3-D detection tasks for low-contrast CT images. We scanned a low-contrast phantom containing four types of signals at three dose levels and used two reconstruction algorithms. We implemented a multislice model observer based on the channelized Hotelling observer (msCHO) with anthropomorphic channels and investigated different internal noise methods. We found a good correlation for all tested model observers. These results suggest that the msCHO can be used as a relevant task-based method to evaluate low-contrast detection for CT and optimize scan protocols to lower dose in an efficient way.

  14. 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.

  15. Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model

    NASA Astrophysics Data System (ADS)

    Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2016-12-01

    In this paper, we study theoretically atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice by using an extended Bose-Hubbard model with intersite repulsions on a 3D optical lattice. Here, the phase and density fluctuations of the boson variable on each site of the optical lattice describe the vector potential and the electric field on each link of the gauge-model lattice, respectively. The target gauge model is different from the standard Wilson-type U(1) gauge-Higgs model because it has plaquette and Higgs interactions with asymmetric couplings in the space-time directions. Nevertheless, the corresponding quantum simulation is still important as it provides us with a platform to study unexplored time-dependent phenomena characteristic of each phase in the general gauge-Higgs models. To determine the phase diagram of the gauge-Higgs model at zero temperature, we perform Monte Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the confinement and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time evolution of an electric flux that initially is put on a straight line connecting two external point charges. We also calculate the potential energy between this pair of charges and obtain the string tension in the confinement phase. Finally, we propose a feasible experimental setup for the atomic simulations of this quantum gauge-Higgs model on the 3D optical lattice. These results may serve as theoretical guides for future experiments.

  16. Implementation of Ensemble Data Assimilation for a Three-Dimensional Radiation Belt Model

    NASA Astrophysics Data System (ADS)

    Godinez, H. C.; Chen, Y.; Shprits, Y.; Kellerman, A. C.; Subbotin, D.

    2013-05-01

    Earth's outer radiation belt is very dynamic and undergoes constant changes due to acceleration, loss, and transport processes of the energetic electrons. In this work the ensemble Kalman filter (EnKF) assimilation method is applied to the Versatile Electron Radiation Belt (VERB) code, a three-dimensional radiation belt model developed at the University of California Los Angeles. The VERB model includes radial, pitch angle, and energy diffusion caused by low-latitude and high-latitude chorus, plasma- spheric hiss, and electromagnetic ion cyclotron (EMIC) waves. Assimi- lation methods based on Kalman filtering have been successfully applied to one-dimensional radial diffusion radiation belt models, where it has been shown that assimilating real observational data into the radiation belt models greatly improves the accuracy of electron PSD estimation. In our work we implement the EnKF for assimilation of real electron PSD data into the VERB model. In particular the assimilation is performed locally along the direction of the dominant diffusion of electrons in the model. This will enable the correct assimilation of data to be consistent with the flow of electrons throughout the model. Two set of assimila- tion experiments are presented. The first is an identical-twin experiment, where artificial data is generated from the same model, with the purpose of validating the assimilation method. In the second set of experiments, real PSD observational data from CRRES are assimilated into VERB in order to improve the model estimation of the electron PSD distribution. The results show that data assimilation significantly improves the accu- racy of the VERB model by efficiently including observations to correct the model PSD estimation.

  17. 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.

  18. Three-dimensional acoustic wave equation modeling based on the optimal finite-difference scheme

    NASA Astrophysics Data System (ADS)

    Cai, Xiao-Hui; Liu, Yang; Ren, Zhi-Ming; Wang, Jian-Min; Chen, Zhi-De; Chen, Ke-Yang; Wang, Cheng

    2015-09-01

    Generally, FD coefficients can be obtained by using Taylor series expansion (TE) or optimization methods to minimize the dispersion error. However, the TE-based FD method only achieves high modeling precision over a limited range of wavenumbers, and produces large numerical dispersion beyond this range. The optimal FD scheme based on least squares (LS) can guarantee high precision over a larger range of wavenumbers and obtain the best optimization solution at small computational cost. We extend the LS-based optimal FD scheme from two-dimensional (2D) forward modeling to three-dimensional (3D) and develop a 3D acoustic optimal FD method with high efficiency, wide range of high accuracy and adaptability to parallel computing. Dispersion analysis and forward modeling demonstrate that the developed FD method suppresses numerical dispersion. Finally, we use the developed FD method to source wavefield extrapolation and receiver wavefield extrapolation in 3D RTM. To decrease the computation time and storage requirements, the 3D RTM is implemented by combining the efficient boundary storage with checkpointing strategies on GPU. 3D RTM imaging results suggest that the 3D optimal FD method has higher precision than conventional methods.

  19. Finite-time vortex singularity and Kolmogorov spectrum in a symmetric three-dimensional spiral model

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, A.; Ng, C. S.; Wang, Xiaogang

    1995-11-01

    A recent analytical model of three-dimensional Euler flows [Phys. Rev. Lett. 69, 2196 (1992)] which exhibits a finite-time vortex singularity is developed further. The initial state is symmetric and contains a velocity null (stagnation point) which is collinear with two vorticity nulls. Under some assumptions, it is shown by asymptotic analysis of the Euler equation that the vorticity blows up at the stagnation point as inverse time in a locally self-similar manner. The spatial structure of the inviscid flow in the vicinity of the singularity involves disparate small scales. The effect of a small but finite viscosity is shown to arrest the formation of the singularity. The presence of spiral structure in the initial conditions leads naturally to the model developed by Lundgren [Phys. Fluids 25, 2193 (1982)] in which the gradual tightening of spirals by differential rotation provides a mechanism for transfer of energy to small spatial scales. It is shown by asymptotic analysis of the Navier-Stokes equation, that a time-average over the lifetime of the spiral vortex in the present model yields the Kolmogorov spectrum.

  20. Model-based labeling, analysis, and three-dimensional visualization from two-dimensional medical images

    NASA Astrophysics Data System (ADS)

    Arata, Louis K.; Dhawan, Atam P.; Thomas, Stephen R.

    1991-07-01

    The computerized analysis and interpretation of three-dimensional medical images is of significant interest for diagnosis as well as for studying pathological processes. Knowledge-based image analysis and interpretation of radiological images can provide a tool for identifying and labeling each part of the image. The authors have developed a knowledge-based biomedical image analysis system for interpreting medical images using an anatomical knowledge base of the appropriate organs. In this paper, the structure of the biomedical image analysis system, along with results from the analysis of images of the human chest cavity, are presented. This approach utilizes an image analysis system with the capability of analyzing the data in both bottom-up (or data driven) and top-down (or model driven) modes to improve the recognition process. After an initial identification is achieved, segmented regions are aggregated and features for these aggregates are recomputed and matched to the model. This process continues until a 'best' match is found for the subject model region. Initial results are encouraging; however, much work remains to be done.

  1. 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.

  2. A Three-Dimensional Simulation Model of Cardiomyocyte Integrating Excitation-Contraction Coupling and Metabolism

    PubMed Central

    Hatano, Asuka; Okada, Jun-ichi; Washio, Takumi; Hisada, Toshiaki; Sugiura, Seiryo

    2011-01-01

    Recent studies have revealed that Ca2+ not only regulates the contraction of cardiomyocytes, but can also function as a signaling agent to stimulate ATP production by the mitochondria. However, the spatiotemporal resolution of current experimental techniques limits our investigative capacity to understand this phenomenon. Here, we created a detailed three-dimensional (3D) cardiomyocyte model to study the subcellular regulatory mechanisms of myocardial energetics. The 3D cardiomyocyte model was based on the finite-element method, with detailed subcellular structures reproduced, and it included all elementary processes involved in cardiomyocyte electrophysiology, contraction, and ATP metabolism localized to specific loci. The simulation results were found to be reproducible and consistent with experimental data regarding the spatiotemporal pattern of cytosolic, intrasarcoplasmic-reticulum, and mitochondrial changes in Ca2+; as well as changes in metabolite levels. Detailed analysis suggested that although the observed large cytosolic Ca2+ gradient facilitated uptake by the mitochondrial Ca2+ uniporter to produce cyclic changes in mitochondrial Ca2+ near the Z-line region, the average mitochondrial Ca2+ changes slowly. We also confirmed the importance of the creatine phosphate shuttle in cardiac energy regulation. In summary, our 3D model provides a powerful tool for the study of cardiac function by overcoming some of the spatiotemporal limitations of current experimental approaches. PMID:22261047

  3. 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.

  4. 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

  5. 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.

  6. 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).

  7. 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.

  8. A three-dimensional PEM fuel cell model with consistent treatment of water transport in MEA

    NASA Astrophysics Data System (ADS)

    Meng, Hua

    In this paper, a three-dimensional PEM fuel cell model with a consistent water transport treatment in the membrane electrode assembly (MEA) has been developed. In this new PEM fuel cell model, the conservation equation of the water concentration is solved in the gas channels, gas diffusion layers, and catalyst layers while a conservation equation of the water content is established in the membrane. These two equations are connected using a set of internal boundary conditions based on the thermodynamic phase equilibrium and flux equality at the interface of the membrane and the catalyst layer. The existing fictitious water concentration treatment, which assumes thermodynamic phase equilibrium between the water content in the membrane phase and the water concentration, is applied in the two catalyst layers to consider water transport in the membrane phase. Since all the other conservation equations are still developed and solved in the single-domain framework without resort to interfacial boundary conditions, the present new PEM fuel cell model is termed as a mixed-domain method. Results from this mixed-domain approach have been compared extensively with those from the single-domain method, showing good accuracy in terms of not only cell performances and current distributions but also water content variations in the membrane.

  9. Modeling human tumor angiogenesis in a three-dimensional culture system.

    PubMed

    Seano, Giorgio; Chiaverina, Giulia; Gagliardi, Paolo Armando; di Blasio, Laura; Sessa, Roberto; Bussolino, Federico; Primo, Luca

    2013-05-23

    The intrinsic complexity of the process of vessel formation limits the efficacy of cellular assays for elucidation of its molecular and pharmacologic mechanisms. We developed an ex vivo three-dimensional (3D) assay of sprouting angiogenesis with arterial explants from human umbilical cords. In this assay, human arterial rings were embedded in basement membrane extract gel, leading to a network of capillarylike structures upon vascular endothelial growth factor (VEGF) A stimulation. The angiogenic outgrowth consisted of endothelial cells, which actively internalized acetylated-low-density lipoprotein, surrounded by pericytes. Computer-assisted quantification of this vascular network demonstrated considerable sensitivity of this assay to several angiogenic inhibitors, including kinase inhibitors and monoclonal antibodies. We also performed targeted gene knockdown on this model by directly infecting explanted umbilical arteries with lentiviruses carrying short-hairpin RNA. Downregulation of VEGFR2 resulted in a significant reduction of the sprouting capability, demonstrating the relevance of human vascular explants for functional genomics studies. Furthermore, a modification of this assay led to development of a 3D model of tumor-driven angiogenesis, in which angiogenic outgrowth was sustained by spheroids of prostate cancer cells in absence of exogenous growth factors. The human arterial ring assay bridges the gap between in vitro endothelial cell and animal model, and is a powerful system for identification of genes and drugs that regulate human angiogenesis.

  10. Combining ZTEM and Magnetotelluric Data to Enhance Three-dimensional Conductivity Models of Porphyry Copper Deposits

    NASA Astrophysics Data System (ADS)

    Lee, B.; Huebert, J.; Abbassi, B.; Liu, L.; Unsworth, M. J.; Richards, J. P.; Cheng, L.; Oldenburg, D.

    2013-12-01

    The airborne Z-Axis Tipper Electromagnetic (ZTEM) method uses natural low frequency electromagnetic signals to determine subsurface electrical conductivity from the surface to a depth of 2 km. It measures the ratio of vertical magnetic field to the horizontal magnetic field with signals in the frequency range 30 -720 Hz. ZTEM is highly effective at determining lateral changes in subsurface conductivity, but does not give the same vertical resolution as the ground-based magnetotelluric (MT) method that measures the ratio of electric to magnetic fields. However, MT surveys require ground contact to measure electric fields and as a consequence are slower to deploy and provide a coarser sampling of conductive features. Since both methods derive the tipper from measured vertical and horizontal magnetic fields, these techniques can be used in a joint approach to create electrical conductivity models. Synthetic MT inversions show that the technique is sensitive to the vertical depth of conductors, complementing the lateral sensitivity of ZTEM. A key application of ZTEM is that metallic sulfide-bearing ore bodies can be resolved because of their high electrical conductivity relative to the host rock. Porphyry copper deposits contain a less distinct geophysical response though, and require additional geologic information. Here we present conductivity models from the Morrison porphyry copper deposit in British Columbia, Canada where the implementation of MT data provides background conductivity and vertical constraints for the three-dimensional ZTEM models.

  11. 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 subj