This thesis utilizes the Immersed Interface Finite Element Method (IIFEM) for shape optimization and material design, while also investigating the modeling and parameterization of lung tissue for Diver Underwater Explosion (UNDEX) simulations. In the first part, a shape optimization scheme utilizing a four-noded rectangular immersed-interface element is presented. This method eliminates the need for interface fitted mesh or mesh morphing, reducing computational costs while maintaining solution accuracy. Analytical design sensitivity analysis is performed to obtain gradients for the optimization formulation, and various parametrization techniques are explored. The effectiveness of the approach is demonstrated through verification and case studies. For material design, the study combines topological shape optimization with IIFEM, providing a computational approach for architecting materials with desired effective properties. Numerical homogenization evaluates effective properties, and level set-based topology optimization evolves boundaries within the unit cell to generate optimal periodic microstructures. The design space is parameterized using radial basis functions, facilitating a gradient-based optimization algorithm for optimal coefficients. The method produces geometries with smooth boundaries and distinct interfaces, demonstrated through numerical examples. The thesis then delves into modeling the mechanical response of lung tissues, particularly focusing on hyperelastic and hyperviscoelastic models. The research adopts a phased approach, emphasizing hyperelastic model parametrization while reserving hyperviscoelastic model parametrization for future studies. Alternative methods are used for parametrization, circumventing direct experimental tests on biological materials. Representative material properties are sourced from literature or refit from existing experimental data, incorporating both empirically derived data and practical values suitable for simulations. Damage parameter quantification relies on asserted quantitative relationships between injury levels and the regions or percentages of affected lung tissue. / Doctor of Philosophy / This research explores the following themes: optimizing shapes, designing materials using repetitive identical building blocks, and understanding how divers' lungs respond to underwater explosions. When computationally analyzing structures with multiple materials, the conventional method involves creating meshes that align with material interfaces, which can be intricate and time-consuming. The Immersed Interface Finite Element Method (IIFEM) is introduced as a computational approach that simplifies this process, utilizing a uniform grid for analysis regardless of interface shape. Consider a plate with a hole or other inclusions. Shape optimization seeks the optimal hole/inclusion shape for withstanding specific loading. Traditional optimization processes necessitate iterative mesh recreation, a step circumvented by employing IIFEM. This technique also extends to creating micro-building blocks of materials, enabling the architectural design of materials with desired qualities. Materials with specific properties, like strength or flexibility can be achieved. This thesis also addresses the challenge of understanding how divers' lungs respond to underwater explosions, a crucial aspect of safety. Advanced computer models are used to mimic the behavior of lung tissue under shock loads. Directly testing materials and tissues can be difficult and restricted. Techniques like gathering data from scientific papers and refitting existing experimental data are utilized to obtain the information needed. Also, it is hard to directly measure how much damage an underwater explosion does to a diver's lungs. Thus, the level of damage was quantified based on assertions about the relationship between different injury severities and how much lung tissue is affected.