Three dimensional modeling of contaminants transportation (oil spill) in Caspian Sea

Nowadays, Caspian Sea is in focus of more attentions than past because of its individualistic as the biggest lake in the world and the existing of very large oil and gas resources within it. Very large scale of oil pollution caused by development of oil exploration and excavation activities not only make problem for coastal facilities but also make severe damage on environment. In the first stage of this research, the location and quality of oil resources in offshore and onshore have been determined and then affected depletion factors on oil spill such as evaporation, emulsification, dissolution, sedimentation and so on have been studied. In second stage, sea hydrodynamics model is offered and tested by determination of governing hydrodynamic equations on sea currents and on pollution transportation in sea surface and by finding out main parameters in these equations such as Coriolis, bottom friction, wind and etc. this model has been calculated by using cell vertex finite volume method in an unstructured mesh domain. According to checked model; sea currents of Caspian Sea in different seasons of the year have been determined and in final stage different scenarios of oil spill movement in Caspian sea on various conditions have been investigated by modeling of three dimensional oil spill movement on surface (affected by sea currents) and on depth (affected by buoyancy, drag and gravity forces) by applying main above mentioned depletion factors.

Three dimensional models of water flow in the Persian Gulf

Persian Gulf region is globally of great importance due to its economical and political reasons. The importance lies in oil sources and sea exports. Geophysical phenomena dominated in the water circulation affected this region is called Monsoon it stretches from African coasts to the half way of Red Seal affected all coasts of Persian Gulf and goes toward east to the Indian ocean. Other essential factors in the water circulation in this region are net evaporation (several meters in per year), high density and high salinity. In this article the effects of wind stress and evaporation in the water circulation in the region will be considered and model equations for wind forces, density, pressure, gradient, and bottom friction for Persian Gulf will be discussed.

Three-dimensional, in-silico breast phantom for multimodality image simulations

We report on the construction of anatomically realistic three-dimensional in-silico breast phantoms with adjustable sizes, shapes and morphologic features. The concept of multiscale spatial resolution is implemented for generating breast tissue images from multiple modalities. Breast epidermal boundary and subcutaneous fat layer is generated by fitting an ellipsoid and 2nd degree polynomials to reconstructive surgical data and ultrasound imaging data. Intraglandular fat is simulated by randomly distributing and orienting adipose ellipsoids within a fibrous region immediately within the dermal layer. Cooper’s ligaments are simulated as fibrous ellipsoidal shells distributed within the subcutaneous fat layer. Individual ductal lobes are simulated following a random binary tree model which is generated based upon probabilistic branching conditions described by ramification matrices, as originally proposed by Bakic et al [3, 4]. The complete ductal structure of the breast is simulated from multiple lobes that extend from the base of the nipple and branch towards the chest wall. As lobe branching progresses, branches are reduced in height and radius and terminal branches are capped with spherical lobular clusters. Biophysical parameters are mapped onto the complete anatomical model and synthetic multimodal images (Mammography, Ultrasound, CT) are generated for phantoms of different adipose percentages (40%, 50%, 60%, and 70%) and are analytically compared with clinical examples. Results demonstrate that the in-silico breast phantom has applications in imaging performance evaluation and, specifically, great utility for solving image registration issues in multimodality imaging.

The three dimensional model with the affection of stratified density (Caspian Sea)

The hydro dynamical actions in big Lakes directly influence dynamic, physical and chemical affairs. The circulation's models and temperature have something to do with the movements of fluids, and analysis for circulation in Caspian sea is because of the lack of observation through which the circulations and out comings are determined. Through the studies, three dimensional simulations (Large- Scale) are planned and performed, according to Smolakiewicz and Margolin works. This is a non- hydrostatic and Boussinesq approximation is used in its formulation is used in its formulation on the basis of Lipps (1990) theorem and curve lines, the fluid is constant adiabatic and stratified, and the wind power is considered zero. The profile of speed according to previous depth and before ridge can be drawn on the basis of density available between northern and southern ridges. The circulation field is drawn from 3 cm/s to 13 cm/s on the plate z= 5 cm , the vertical changes of speed on the plate is 0.02 m/s. Vertical profile , horizontal speed in previous on, and after the ridges on are drawn on different spaces. It changes from 0.5 cm/s to 1 cm/s before ridges.

Three dimensional visualization of the World Wide Web

Although large-scale public hypermedia structures such as the World Wide Web are popularly referred to as "cyberspace", the extent to which they constitute a space in the everyday sense of the word is questionable. This paper reviews recent work in the area of three dimensional (3D) visualization of the Web that has attempted to depict it in the form of a recognizable space; in other words, as a navigable landscape that may be visibly populated by its users. Our review begins by introducing a range of visualizations that address different aspects of using the Web. These include visualizations of Web structure, especially of links, that act as 3D maps; browsing history; searches; evolution of the Web; and the presence and activities of multiple users. We then summarize the different techniques that are employed by these visualizations. We conclude with a discussion of key challenges for the future.

Three dimensional circulation of water with variable wind in the Caspian Sea

This research is based on a numerical model for forecasting the three-dimensional behavior of (sea) water motion due to the effect of a variable wind velocity. The results obtained are then analyzed and compared with observation. This model is based on the equations that overcome the current and distribution of temperature by applying the method of finite difference with assuming Δx, Δy as constant and Δz, variable. The model is based on the momentum equation, continuity equation and thermodynamic energy equation and tension at the surface and middle layers and bottom stress. The horizontal and vertical eddy viscosity and thermal diffusivity coefficients we used in accordance with that of the Bennet on Outario Lake (1977). Considering the Caspian Sea dimension in numerical model the Coriolis parameter used with β effects and the approximation Boussines have been used. For the program controlling some simple experiment with boundary condition similar to that of the Caspian Sea have been done. For modeling the Caspian Sea the grid of the field was done as follows: At horizontal surface grid size is 10×10km extension and at vertical in 10 layers with varying thickness from surface to bed respectively as: 5, 10, 20, 3, 50, 100, 150, 200, 25, 500 and higher. The data of wind as velocity، direction and temperature of water related to 15th September 1995 at 6،12 and 18 o’clock were obtained from synoptic station at the Caspian Sea shore and the research marine of Haji Alief. The information concerning shore wind was measured and by the method of SPM (shore protection manual) was transferred to far shore winds through interpolation and by use of inverse square distance of position distribution of the wind velocity at the Caspian surface field was obtained. The model has been evaluated according to the reports and observations. Through studying the position of the current in different layers، the velocity in the cross section in the northern، southern and the middle layers، will be discussed. The results reveal the presence of the circulation cells in the three above mentioned areas. The circulation with depth is reduced too. The results obtained through the numerical solution of the temperature equation have been compared with the observation. The temperature change in different layers in cross section illustrates the relative accordance of the model mentioned.

Coupling of Chemical Kinetics with Computational Fluid Dynamics in a Three-Dimensional Engine Model

The role of computer modeling has grown recently to integrate itself as an inseparable tool to experimental studies for the optimization of automotive engines and the development of future fuels. Traditionally, computer models rely on simplified global reaction steps to simulate the combustion and pollutant formation inside the internal combustion engine. With the current interest in advanced combustion modes and injection strategies, this approach depends on arbitrary adjustment of model parameters that could reduce credibility of the predictions. The purpose of this study is to enhance the combustion model of KIVA, a computational fluid dynamics code, by coupling its fluid mechanics solution with detailed kinetic reactions solved by the chemistry solver, CHEMKIN. As a result, an engine-friendly reaction mechanism for n-heptane was selected to simulate diesel oxidation. Each cell in the computational domain is considered as a perfectly-stirred reactor which undergoes adiabatic constant- volume combustion. The model was applied to an ideally-prepared homogeneous- charge compression-ignition combustion (HCCI) and direct injection (DI) diesel combustion. Ignition and combustion results show that the code successfully simulates the premixed HCCI scenario when compared to traditional combustion models. Direct injection cases, on the other hand, do not offer a reliable prediction mainly due to the lack of turbulent-mixing model, inherent in the perfectly-stirred reactor formulation. In addition, the model is sensitive to intake conditions and experimental uncertainties which require implementation of enhanced predictive tools. It is recommended that future improvements consider turbulent-mixing effects as well as optimization techniques to accurately simulate actual in-cylinder process with reduced computational cost. Furthermore, the model requires the extension of existing fuel oxidation mechanisms to include pollutant formation kinetics for emission control studies.

Three dimensional study to quantify the relationship between facial hard and soft tissue movement as a result of orthognathic surgery

Introduction Prediction of soft tissue changes following orthognathic surgery has been frequently attempted in the past decades. It has gradually progressed from the classic “cut and paste” of photographs to the computer assisted 2D surgical prediction planning; and finally, comprehensive 3D surgical planning was introduced to help surgeons and patients to decide on the magnitude and direction of surgical movements as well as the type of surgery to be considered for the correction of facial dysmorphology. A wealth of experience was gained and numerous published literature is available which has augmented the knowledge of facial soft tissue behaviour and helped to improve the ability to closely simulate facial changes following orthognathic surgery. This was particularly noticed following the introduction of the three dimensional imaging into the medical research and clinical applications. Several approaches have been considered to mathematically predict soft tissue changes in three dimensions, following orthognathic surgery. The most common are the Finite element model and Mass tensor Model. These were developed into software packages which are currently used in clinical practice. In general, these methods produce an acceptable level of prediction accuracy of soft tissue changes following orthognathic surgery. Studies, however, have shown a limited prediction accuracy at specific regions of the face, in particular the areas around the lips. Aims The aim of this project is to conduct a comprehensive assessment of hard and soft tissue changes following orthognathic surgery and introduce a new method for prediction of facial soft tissue changes.   Methodology The study was carried out on the pre- and post-operative CBCT images of 100 patients who received their orthognathic surgery treatment at Glasgow dental hospital and school, Glasgow, UK. Three groups of patients were included in the analysis; patients who underwent Le Fort I maxillary advancement surgery; bilateral sagittal split mandibular advancement surgery or bimaxillary advancement surgery. A generic facial mesh was used to standardise the information obtained from individual patient’s facial image and Principal component analysis (PCA) was applied to interpolate the correlations between the skeletal surgical displacement and the resultant soft tissue changes. The identified relationship between hard tissue and soft tissue was then applied on a new set of preoperative 3D facial images and the predicted results were compared to the actual surgical changes measured from their post-operative 3D facial images. A set of validation studies was conducted. To include: • Comparison between voxel based registration and surface registration to analyse changes following orthognathic surgery. The results showed there was no statistically significant difference between the two methods. Voxel based registration, however, showed more reliability as it preserved the link between the soft tissue and skeletal structures of the face during the image registration process. Accordingly, voxel based registration was the method of choice for superimposition of the pre- and post-operative images. The result of this study was published in a refereed journal. • Direct DICOM slice landmarking; a novel technique to quantify the direction and magnitude of skeletal surgical movements. This method represents a new approach to quantify maxillary and mandibular surgical displacement in three dimensions. The technique includes measuring the distance of corresponding landmarks digitized directly on DICOM image slices in relation to three dimensional reference planes. The accuracy of the measurements was assessed against a set of “gold standard” measurements extracted from simulated model surgery. The results confirmed the accuracy of the method within 0.34mm. Therefore, the method was applied in this study. The results of this validation were published in a peer refereed journal. • The use of a generic mesh to assess soft tissue changes using stereophotogrammetry. The generic facial mesh played a major role in the soft tissue dense correspondence analysis. The conformed generic mesh represented the geometrical information of the individual’s facial mesh on which it was conformed (elastically deformed). Therefore, the accuracy of generic mesh conformation is essential to guarantee an accurate replica of the individual facial characteristics. The results showed an acceptable overall mean error of the conformation of generic mesh 1 mm. The results of this study were accepted for publication in peer refereed scientific journal. Skeletal tissue analysis was performed using the validated “Direct DICOM slices landmarking method” while soft tissue analysis was performed using Dense correspondence analysis. The analysis of soft tissue was novel and produced a comprehensive description of facial changes in response to orthognathic surgery. The results were accepted for publication in a refereed scientific Journal. The main soft tissue changes associated with Le Fort I were advancement at the midface region combined with widening of the paranasal, upper lip and nostrils. Minor changes were noticed at the tip of the nose and oral commissures. The main soft tissue changes associated with mandibular advancement surgery were advancement and downward displacement of the chin and lower lip regions, limited widening of the lower lip and slight reversion of the lower lip vermilion combined with minimal backward displacement of the upper lip were recorded. Minimal changes were observed on the oral commissures. The main soft tissue changes associated with bimaxillary advancement surgery were generalized advancement of the middle and lower thirds of the face combined with widening of the paranasal, upper lip and nostrils regions. In Le Fort I cases, the correlation between the changes of the facial soft tissue and the skeletal surgical movements was assessed using PCA. A statistical method known as ’Leave one out cross validation’ was applied on the 30 cases which had Le Fort I osteotomy surgical procedure to effectively utilize the data for the prediction algorithm. The prediction accuracy of soft tissue changes showed a mean error ranging between (0.0006mm±0.582) at the nose region to (-0.0316mm±2.1996) at the various facial regions.

Cell-cell communication in three dimensional microenvironments

Cellular behavior is dependent on a variety of extracellular cues required for normal tissue function, wound healing, and activation of the immune system. Removed from their in vivo microenvironment and cultured in vitro, cells lose many environmental cues and that may result in abberant behavior, making it difficult to study cellular processes. In order to mimic native tissue environments, optical tweezer and microfluidic technologies were used to place cells within defined areas of the culture environment. To provide three dimensional supports found in natural tissues, hydrogel scaffolds of poly (ethylene glycol) diacrylate and the basement membrane matrix Matrigel were used. Optical tweezer technology allowed precision placement and formation of homotypic and heterotypic arrays of human U937, HEK 293, and porcine mesenchymal stem cells. Alternatively, two microfluidic devices were designed to pattern Matrigel scaffolds. The first microfluidic device utilized laminar flow to spatially pattern multiple cell types within the device. Gradients of soluble molecules were then be formed and manipulated across the Matrigel scaffolds. Patterning Matrigel using laminar flow techniques require microfluidic expertise and do not produce consistent patterning conditions, limiting their use difficult in most cell culture laboratories. Thus, a buried Matrigel polydimethylsiloxane (PDMS) device was developed for spatial patterning of biological scaffolds. Matrigel is injected into micron sized channels of PDMS fabricated by soft lithography and allowed to thermally cure. Following curing, a second PDMS device was placed on top of the buried Matrigel channels to support media flow. In order to validate these systems, a cell-cell communication model system was developed utilizing LPS and TNFα signaling with fluorescent reporter systems to monitor communication in real time. We demonstrated the utility of microfluidic devices to support the cell-cell communication model system by co culturing three cell types within Matrigel scaffolds and monitoring signaling activity via fluorescent reporters.

Probabilistic Evaluation of Three-Dimensional Reconstructions from X-Ray Images Spanning a Limited Angle

An important part of computed tomography is the calculation of a three-dimensional reconstruction of an object from series of X-ray images. Unfortunately, some applications do not provide sufficient X-ray images. Then, the reconstructed objects no longer truly represent the original. Inside of the volumes, the accuracy seems to vary unpredictably. In this paper, we introduce a novel method to evaluate any reconstruction, voxel by voxel. The evaluation is based on a sophisticated probabilistic handling of the measured X-rays, as well as the inclusion of a priori knowledge about the materials that the object receiving the X-ray examination consists of. For each voxel, the proposed method outputs a numerical value that represents the probability of existence of a predefined material at the position of the voxel while doing X-ray. Such a probabilistic quality measure was lacking so far. In our experiment, false reconstructed areas get detected by their low probability. In exact reconstructed areas, a high probability predominates. Receiver Operating Characteristics not only confirm the reliability of our quality measure but also demonstrate that existing methods are less suitable for evaluating a reconstruction.

Three dimensional numerical simulation of thermohaline currents of the Persian Gulf

Observational data and a three dimensional numerical model (POM) are used to investigate the Persian Gulf outflow structure and its spreading pathway into the Oman Sea. The model is based on orthogonal curvilinear coordinate system in horizontal and train following coordinate (sigma coordinate) system in vertical. In the simulation, the horizontal diffusivity coefficients are calculated form Smogorinsky diffusivity formula and the eddy vertical diffusivities are obtained from a second turbulence closure model (namely Mellor-Yamada level 2.5 model of turbulence). The modeling area includes the east of the Persian Gulf, the Oman Sea and a part of the north-east of the Indian Ocean. In the model, the horizontal grid spacing was assumed to be about 3.5 km and the number of vertical levels was set to 32. The simulations show that the mean salinity of the PG outflow does not change substantially during the year and is about 39 psu, while its temperature exhibits seasonal variations. These lead to variations in outflow density in a way that is has its maximum density in late winter (March) and its minimum in mid-summer (August). At the entrance to the Oman Sea, the PG outflow turns to the right due to Coriolis Effect and falls down on the continental slope until it gains its equilibrium depth. The highest density of the outflow during March causes it to sink more into the deeper depths in contrast to that of August which the density is the lowest one. Hence, the neutral buoyancy depths of the outflow are about 500 m and 250 m for March and August respectively. Then, the outflow spreads in its equilibrium depths in the Oman Sea in vicinity of western and southern boundaries until it approach the Ras al Hamra Cape where the water depth suddenly begins to increase. Therefore, during March, the outflow that is deeper and wider relative to August, is more affected by the steep slope topography and as a result of vortex stretching mechanism and conservation of potential vorticity it separates from the lateral boundaries and finally forms an anti-cyclonic eddy in the Oman Sea. But during August the outflow moves as before in vicinity of lateral boundaries. In addition, the interaction of the PG outflow with tide in the Strait of Hormuz leads to intermittency in outflow movement into the Oman Sea and it could be the major reason for generations of Peddy (Peddies) in the Oman Sea.

Fully Anisotropic Solution of the Three Dimensional Boltzmann Transport Equation

The development of accurate modeling techniques for nanoscale thermal transport is an active area of research. Modern day nanoscale devices have length scales of tens of nanometers and are prone to overheating, which reduces device performance and lifetime. Therefore, accurate temperature profiles are needed to predict the reliability of nanoscale devices. The majority of models that appear in the literature obtain temperature profiles through the solution of the Boltzmann transport equation (BTE). These models often make simplifying assumptions about the nature of the quantized energy carriers (phonons). Additionally, most previous work has focused on simulation of planar two dimensional structures. This thesis presents a method which captures the full anisotropy of the Brillouin zone within a three dimensional solution to the BTE. The anisotropy of the Brillouin zone is captured by solving the BTE for all vibrational modes allowed by the Born Von-Karman boundary conditions.

Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.