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Motivated by the wide application of advanced thermal barrier coatings with ultra low thermal conductivity in gas turbines, this thesis focuses on the mechanisms of thermal transport in crystalline material containing defects and on the structure formation process during processing by thermal spraying techniques. A better understanding of thermal properties and the microstructure formation mechanisms for thermal barrier coatings is a major advance in science and an important ingredient in future optimization and improvement of the performance of these engineering materials for industrial applications. This is accomplished by the large-scale molecular dynamics simulations because of its atomistic resolution, which helps to reveal mechanisms that otherwise cannot be easily observed in experiments. In the first part of this thesis, the aim is to develop a fundamental understanding of thermal transport properties especially influenced by the presence of crystallographic defects. Special focus is placed on the influence of defect structures on thermal transport properties of materials, such as nano-voids, vacancies, polydisperse particles and grain boundaries. Combining with the plane wave assumption, the spectral energy densities are then analyzed by means of molecular dynamics and lattice dynamics calculations to reveal the dominant mechanisms of thermal transport in solids. As the formation of defect structures in thermal barrier coatings is highly dependent on the manufacturing process, this thesis further explores the formation mechanisms of the coatings under varying conditions to gain a better insight and to support the future knowledge based design of such coating systems. Large-scale molecular dynamics simulations are conducted to investigate the microstructure formation mechanism by spraying hot nano-particles onto a cooled substrate. In order to evaluate the influence of processing parameters on the morphology of the coating structure, simulations with different parameters, such as initial temperature, size and velocity of the sprayed particles are conducted. The results reveal the dependence of microstructures formation mechanisms on thermal spraying parameters, and more importantly provide elementary insight into the microstructure formation mechanisms at the atomistic scale.