Visualizing the Simulation of 3-D Underwater Sensor Networks

The majority of sensor network research deals with land-based networks, which are essentially two-dimensional, and thus the majority of simulation and animation tools also only handle such networks. Underwater sensor networks on the other hand, are essentially 3D networks because the depth at which a sensor node is located needs to be considered as well. Due to that additional dimension, specialized tools need to be used when conducting simulations for experimentation. The School of Engineering’s Underwater Sensor Network (UWSN) lab is conducting research on underwater sensor networks and requires simulation tools for 3D networks. The lab has extended NS-2, a widely used network simulator, so that it can simulate three-dimensional networks. However, NAM, a widely used network animator, currently only supports two-dimensional networks and no extensions have been implemented to give it three-dimensional capabilities. In this project, we develop a network visualization tool that functions similarly to NAM but is able to render network environments in full 3-D. It is able to take as input a NS-2 trace file (the same file taken as input by NAM), create the environment, position the sensor nodes, and animate the events of the simulation. Further, the visualization tool is easy to use, especially friendly to NAM users, as it is designed to follow the interfaces and functions similar to NAM. So far, the development has fulfilled the basic functionality. Future work includes fully functional capabilities for visualization and much improved user interfaces.

Development of a SPECT -based three-dimensional treatment planner for radionuclide therapy with iodine -131

Accurate calculation of absorbed dose to target tumors and normal tissues in the body is an important requirement for establishing fundamental dose-response relationships for radioimmunotherapy. Two major obstacles have been the difficulty in obtaining an accurate patient-specific 3-D activity map in-vivo and calculating the resulting absorbed dose. This study investigated a methodology for 3-D internal dosimetry, which integrates the 3-D biodistribution of the radionuclide acquired from SPECT with a dose-point kernel convolution technique to provide the 3-D distribution of absorbed dose. Accurate SPECT images were reconstructed with appropriate methods for noise filtering, attenuation correction, and Compton scatter correction. The SPECT images were converted into activity maps using a calibration phantom. The activity map was convolved with an $\sp{131}$I dose-point kernel using a 3-D fast Fourier transform to yield a 3-D distribution of absorbed dose. The 3-D absorbed dose map was then processed to provide the absorbed dose distribution in regions of interest. This methodology can provide heterogeneous distributions of absorbed dose in volumes of any size and shape with nonuniform distributions of activity. Comparison of the activities quantitated by our SPECT methodology to true activities in an Alderson abdominal phantom (with spleen, liver, and spherical tumor) yielded errors of $-$16.3% to 4.4%. Volume quantitation errors ranged from $-$4.0 to 5.9% for volumes greater than 88 ml. The percentage differences of the average absorbed dose rates calculated by this methodology and the MIRD S-values were 9.1% for liver, 13.7% for spleen, and 0.9% for the tumor. Good agreement (percent differences were less than 8%) was found between the absorbed dose due to penetrating radiation calculated from this methodology and TLD measurement. More accurate estimates of the 3-D distribution of absorbed dose can be used as a guide in specifying the minimum activity to be administered to patients to deliver a prescribed absorbed dose to tumor without exceeding the toxicity limits of normal tissues. ^

A Variational Stereo Method for the Three-Dimensional Reconstruction of Ocean Waves

We develop a novel remote sensing technique for the observation of waves on the ocean surface. Our method infers the 3-D waveform and radiance of oceanic sea states via a variational stereo imagery formulation. In this setting, the shape and radiance of the wave surface are given by minimizers of a composite energy functional that combines a photometric matching term along with regularization terms involving the smoothness of the unknowns. The desired ocean surface shape and radiance are the solution of a system of coupled partial differential equations derived from the optimality conditions of the energy functional. The proposed method is naturally extended to study the spatiotemporal dynamics of ocean waves and applied to three sets of stereo video data. Statistical and spectral analysis are carried out. Our results provide evidence that the observed omnidirectional wavenumber spectrum S(k) decays as k-2.5 is in agreement with Zakharov's theory (1999). Furthermore, the 3-D spectrum of the reconstructed wave surface is exploited to estimate wave dispersion and currents.

Effect of Aspect Ratio on the Three-Dimensional Global Instability Analysis of Incompressible Open Cavity Flows

The stability analysis of open cavity flows is a problem of great interest in the aeronautical industry. This type of flow can appear, for example, in landing gears or auxiliary power unit configurations. Open cavity flows is very sensitive to any change in the configuration, either physical (incoming boundary layer, Reynolds or Mach numbers) or geometrical (length to depth and length to width ratio). In this work, we have focused on the effect of geometry and of the Reynolds number on the stability properties of a threedimensional spanwise periodic cavity flow in the incompressible limit. To that end, BiGlobal analysis is used to investigate the instabilities in this configuration. The basic flow is obtained by the numerical integration of the Navier-Stokes equations with laminar boundary layers imposed upstream. The 3D perturbation, assumed to be periodic in the spanwise direction, is obtained as the solution of the global eigenvalue problem. A parametric study has been performed, analyzing the stability of the flow under variation of the Reynolds number, the L/D ratio of the cavity, and the spanwise wavenumber β. For consistency, multidomain high order numerical schemes have been used in all the computations, either basic flow or eigenvalue problems. The results allow to define the neutral curves in the range of L/D = 1 to L/D = 3. A scaling relating the frequency of the eigenmodes and the length to depth ratio is provided, based on the analysis results.

Reduced order modeling of three dimensional external aerodynamic flows

A method is presented to construct computationally efficient reduced-order models (ROMs) of three-dimensional aerodynamic flows around commercial aircraft components. The method is based on the proper orthogonal decomposition (POD) of a set of steady snapshots, which are calculated using an industrial solver based on some Reynolds averaged Navier-Stokes (RANS) equations. The POD-mode amplitudes are calculated by minimizing a residual defined from the Euler equations, even though the snapshots themselves are calculated from viscous equations. This makes the ROM independent of the peculiarities of the solver used to calculate the snapshots. Also, both the POD modes and the residual are calculated using points in the computational mesh that are concentrated in a close vicinity of the aircraft, which constitute a much smaller number than the total number of mesh points. Despite these simplifications, the method provides quite good approximations of the flow variables distributions in the whole computational domain, including the boundary layer attached to the aircraft surface and the wake. Thus, the method is both robust and computationally efficient, which is checked considering the aerodynamic flow around a horizontal tail plane, in the transonic range 0.4?Mach number?0.8, ?3°?angle of attack?3°.

Edge Detection by Adaptive Splitting II. The Three-Dimensional Case

In Llanas and Lantarón, J. Sci. Comput. 46, 485–518 (2011) we proposed an algorithm (EDAS-d) to approximate the jump discontinuity set of functions defined on subsets of ℝ d . This procedure is based on adaptive splitting of the domain of the function guided by the value of an average integral. The above study was limited to the 1D and 2D versions of the algorithm. In this paper we address the three-dimensional problem. We prove an integral inequality (in the case d=3) which constitutes the basis of EDAS-3. We have performed detailed computational experiments demonstrating effective edge detection in 3D function models with different interface topologies. EDAS-1 and EDAS-2 appealing properties are extensible to the 3D case

A Three-Dimensional B.I.E.M. Program

The program PECET (Boundary Element Program in Three-Dimensional Elasticity) is presented in this paper. This program, written in FORTRAN V and implemen ted on a UNIVAC 1100,has more than 10,000 sentences and 96 routines and has a lot of capabilities which will be explained in more detail. The object of the program is the analysis of 3-D piecewise heterogeneous elastic domains, using a subregionalization process and 3-D parabolic isopara, metric boundary elements. The program uses special data base management which will be described below, and the modularity followed to write it gives a great flexibility to the package. The Method of Analysis includes an adaptive integration process, an original treatment of boundary conditions, a complete treatment of body forces, the utilization of a Modified Conjugate Gradient Method of solution and an original process of storage which makes it possible to save a lot of memory.

3-D modeling of perimeter recombination in GaAs diodes and its influence on concentrator solar cells

This paper describes a complete modelling of the perimeter recombination of GaAs diodes which solves most unknowns and suppresses the limitations of previous models. Because of the three dimensional nature of the implemented model, it is able to simulate real devices. GaAs diodes on two epiwafers with different base doping levels, sizes and geometries, namely square and circular are manufactured. The validation of the model is achieved by fitting the experimental measurements of the dark IV curve of the manufactured GaAs diodes. A comprehensive 3-D description of the occurring phenomena affecting the perimeter recombination is supplied with the help of the model. Finally, the model is applied to concentrator GaAs solar cells to assess the impact of their doping level, size and geometry on the perimeter recombination.

Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain

The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.

Three-dimensional reconstruction of the recombinant type 3 ryanodine receptor and localization of its amino terminus

Recombinant type 3 ryanodine receptor (RyR3) has been purified in quantities sufficient for structural characterization by cryoelectron microscopy and three-dimensional (3D) reconstruction. Two cDNAs were prepared and expressed in HEK293 cells, one encoding the wild-type RyR3 and the other encoding RyR3 containing glutathione S-transferase (GST) fused to its amino terminus (GST-RyR3). RyR3 was purified from detergent-solubilized transfected cells by affinity chromatography using 12.6-kDa FK506-binding protein in the form of a GST fusion as the affinity ligand. Purification of GST-RyR3 was achieved by affinity chromatography by using glutathione-Sepharose. Purified recombinant RyR3 and GST-RyR3 proteins exhibited high-affinity [3H]ryanodine binding that was sensitive to activation by Ca2+ and caffeine and to inhibition by Mg2+. 3D reconstructions of both recombinant RyR3 and GST-RyR3 appeared very similar to that of the native RyR3 purified from bovine diaphragm. Comparison of the 3D reconstructions of RyR3 and GST-RyR3 revealed that the GST domains and, hence, the amino termini of the RyR3 subunits are located in the “clamp” structures that form the corners of the square-shaped cytoplasmic region of homotetrameric RyR3. This study describes the 3D reconstruction of a recombinant ryanodine receptor and it demonstrates the potential of this technology for characterizing functional and structural perturbations introduced by site-directed mutagenesis.

Three-dimensional inverse modelling of magnetic anomaly sources based on a genetic algorithm.

We present a modelling method to estimate the 3-D geometry and location of homogeneously magnetized sources from magnetic anomaly data. As input information, the procedure needs the parameters defining the magnetization vector (intensity, inclination and declination) and the Earth's magnetic field direction. When these two vectors are expected to be different in direction, we propose to estimate the magnetization direction from the magnetic map. Then, using this information, we apply an inversion approach based on a genetic algorithm which finds the geometry of the sources by seeking the optimum solution from an initial population of models in successive iterations through an evolutionary process. The evolution consists of three genetic operators (selection, crossover and mutation), which act on each generation, and a smoothing operator, which looks for the best fit to the observed data and a solution consisting of plausible compact sources. The method allows the use of non-gridded, non-planar and inaccurate anomaly data and non-regular subsurface partitions. In addition, neither constraints for the depth to the top of the sources nor an initial model are necessary, although previous models can be incorporated into the process. We show the results of a test using two complex synthetic anomalies to demonstrate the efficiency of our inversion method. The application to real data is illustrated with aeromagnetic data of the volcanic island of Gran Canaria (Canary Islands).

Methods of Visualization and Analysis of Cardiac Depolarization in the Three Dimensional Space

Research analysis of electrocardiograms (ECG) today is carried out mostly using time depending signals of different leads shown in the graphs. Definition of ECG parameters is performed by qualified personnel, and requiring particular skills. To support decoding the cardiac depolarization phase of ECG there are methods to analyze space-time convolution charts in three dimensions where the heartbeat is described by the trajectory of its electrical vector. Based on this, it can be assumed that all available options of the classical ECG analysis of this time segment can be obtained using this technique. Investigated ECG visualization techniques in three dimensions combined with quantitative methods giving additional features of cardiac depolarization and allow a better exploitation of the information content of the given ECG signals.

A proposed scheme for comprehensive characterization of the measured geometric distortion in magnetic resonance imaging using a three-dimensional phantom

Recently, a 3-dimensional phantom that can provide a comprehensive, accurate and complete measurement of the geometric distortion in MRI has been developed. In this paper, a scheme for characterizing the measured geometric distortion using the 3-D phantom is described. In the proposed scheme, a number of quantitative measures are developed and used to characterize the geometric distortion. These measures encompass the overall and spatial aspects of the geometric distortion. Two specific types of volume of interest, rectangular parallelepipeds (including cubes) and spheres are considered in the proposed scheme. As an illustration, characterization of the geometric distortion in a Siemens 1.5T Sonata MRI system using the proposed scheme is presented. As shown, the proposed scheme provides a comprehensive assessment of the geometric distortion. The scheme can be potentially used as a standard procedure for the assessment of geometric distortion in MRI. (C) 2004 American Association of Physicists in Medicine.

3-D magnetic resonance angiography versus conventional angiography in peripheral arterial disease: Pilot study

Angiography is usually performed as the preoperative road map for those requiring revascularization for lower extremity peripheral arterial disease (PAD). The alternative investigations are ultrasound, 3-D magnetic resonance angiography (3-D MRA) and computed tomography angiography. This pilot study aimed to assess whether 3-D MRA could replace the gold standard angiography in preoperative planning. Eight patients considered for aortoiliac or infrainguinal arterial bypass surgery were recruited. All underwent both imaging modalities within 7 days. A vascular surgeon and a radiologist each reported on the images from both the 3-D MRA and the angiography, with blinding to patient details and each others reports. Comparisons were made between the reports for the angiographic and the 3-D MRA images, and between the reports of the vascular surgeon and the radiologist. Compared to the gold standard angiogram, 3-D MRA had a sensitivity of 77% and specificity of 94% in detecting occlusion, and a sensitivity of 72% and specificity of 90% in differentiating high grade (> 50%) versus low grade (< 50%) stenoses. There was an overall concordance of 78% between the two investigations with a range of 62% in the peroneal artery to 94% in the aorta. 3-D MRA showed flow in 23% of cases where conventional angiography showed no flow. In the present pilot study, 3-D MRA had reasonable concordance with the gold standard angiography, depending on the level of the lesion. At times it showed vessel flow where occlusion was shown on conventional angiogram. 3-D MRA in peripheral vascular disease is challenging the gold standard, but is inconsistent at present.

Changes in three dimensional lumbo-pelvic kinematics and trunk muscle activity with speed and mode of locomotion

Background Control of the trunk is critical for locomotor efficiency. However, investigations of trunk muscle activity and three-dimensional lumbo-pelvic kinematics during walking and running remain scarce. Methods. Gait parameters and three-dimensional lumbo-pelvic kinematics were recorded in seven subjects. Electromyography recordings of abdominal and paraspinal muscles were made using fine-wire and surface electrodes as subjects walked on a treadmill at 1 and 2 ms(-1) and ran at 2, 3, 4 and 5 ms(-1). Findings. Kinematic data indicate that the amplitude but not timing of lumbo-pelvic motion changes with locomotor speed. Conversely, a change in locomotor mode is associated with temporal but not spatial adaptation in neuromotor strategy. That is, peak transverse plane lumbo-pelvic rotation occurs at foot strike during walking but prior to foot strike during running. Despite this temporal change, there is a strong correlation between the amplitude of transverse plane lumbo-pelvic rotation and stride length during walking and running. In addition, Jumbo-pelvic motion was asymmetrical during all locomotor tasks. Trunk muscle electromyography occurred biphasically in association with foot strike. Transversus abdominis was tonically active with biphasic modulation. Consistent with the kinematic data, electromyography activity of the abdominal muscles and the superficial fibres of multifidus increased with locomotor speed, and timing of peak activity of superficial multifidus and obliquus externus abdominis was modified in association with the temporal adaptation in lumbo-pelvic motion with changes in locomotor mode. Interpretation. These data provide evidence of the association between lumbo-pelvic motion and trunk muscle activity during locomotion at different speeds and modes. (c) 2005 Elsevier Ltd. All rights reserved.