<p>Interfaces play a dominant role in governing the response of many biological systems and they pose many challenges to traditional finite element. For sharp-interface model, traditional finite element methods necessitate the finite element mesh to align with surfaces of discontinuities. Diffuse-interface model replaces the sharp interface with continuous variations of an order parameter resulting in significant computational effort. To overcome these difficulties, we focus on developing a computationally efficient spline-based finite element method for interface problems.</p><p>A key challenge while employing B-spline basis functions in finite-element methods is the robust imposition of Dirichlet boundary conditions. We begin by examining weak enforcement of such conditions for B-spline basis functions, with application to both second- and fourth-order problems based on Nitsche's approach. The use of spline-based finite elements is further examined along with a Nitsche technique for enforcing constraints on an embedded interface. We show that how the choice of weights and stabilization parameters in the Nitsche consistency terms has a great influence on the accuracy and robustness of the method. In the presence of curved interface, to obtain optimal rates of convergence we employ a hierarchical local refinement approach to improve the geometrical representation of interface. </p><p>In multiple dimensions, a spline basis is obtained as a tensor product of the one-dimensional basis. This necessitates a rectangular grid that cannot be refined locally in regions of embedded interfaces. To address this issue, we develop an adaptive spline-based finite element method that employs hierarchical refinement and coarsening techniques. The process of refinement and coarsening guarantees linear independence and remains the regularity of the basis functions. We further propose an efficient data transfer algorithm during both refinement and coarsening which yields to accurate results.</p><p>The adaptive approach is applied to vesicle modeling which allows three-dimensional simulation to proceed efficiently. In this work, we employ a continuum approach to model the evolution of microdomains on the surface of Giant Unilamellar Vesicles. The chemical energy is described by a Cahn-Hilliard type density functional that characterizes the line energy between domains of different species. The generalized Canham-Helfrich-Evans model provides a description of the mechanical energy of the vesicle membrane. This coupled model is cast in a diffuse-interface form using the phase-field framework. The effect of coupling is seen through several numerical examples of domain formation coupled to vesicle shape changes.</p> / Dissertation

Meshless methods provide a highly continuous approximation field, convenient for thin structures like shells. Nevertheless, the lack of Kronecker Delta property makes the formulation of essential boundary conditions not straightforward, as the trial and test fields cannot be tailored to boundary values. Similar problem arise when different approximation regions must be joined, in a multi-region problem, such as kinks, folds or joints. This work presents three approaches to impose both kinematic conditions: the well known Lagrange Multiplier method, used since the beginning of the Element Free Galerkin method; a pure penalty approach; and the recently rediscovered alternative of Nitsche\'s Method. We use the EFG discretization technique for thick Reissner-Mindlin shells and adapt the weak form as to separate displacement and rotational degrees of freedom and obtain suitable and separate stabilization parameters. This approach enables the modeling of discontinuous shells and local refinement on multi-region problems. / Métodos sem malha geram campos de aproximação com alta continuidade, convenientes para estruturas finas como cascas. No entanto, a ausência da propriedade de Delta de Kronecker dificulta a formulação de condições essenciais de contorno, já que os campos de aproximação e teste não podem ser moldados aos valores de contorno. Um problema similar aparece quando diferentes regiões de aproximação precisam ser juntadas em um problema multi-regiões como dobras, vincos ou junções. Este trabalho apresenta três métodos de imposição ambas condições cinemáticas: o já conhecido método dos multiplicadores de Lagrange, usado desde o começo do método de Galekin sem elementos (EFG); uma abordagem de penalidade pura; e o recentemente redescoberto método de Nitsche. Nós usamos a técnica de discretização com EFG para cascas espessas de Reissner-Mindlin e adaptamos a forma fraca de forma a separar graus de liberdade de deslocamento e rotação e obter coeficientes de estabilização diferentes e apropriados. Essa abordagem permite a modelagem de cascas discontínuas e o refinamento local em problemas multi-regiões.

1 Abstract: Time-dependent and three-dimensional flow of Newtonian fluid is studied in context of two biomechanical applications, flow in cerebral aneurysms and flow in stenotic valves. In the first part of the thesis, the computational meshes obtained from the medical imaging techniques are used for the computation of hemodynamic parameters associated with the rupture potency of the cerebral aneurysms. The main result is the computation within twenty geometries of aneurysms. It is shown that the aneurysm size has more important role in wall shear stress distribution than the fact whether the aneurysm is ruptured or unruptured. The second part of the thesis is addressed to the flow in stenotic valves. It is shown that the method cur- rently used in medical practice is based on assumptions which are too restrictive to be apply to blood flow in the real case. The full continuum mechanics model is presented with physiologically relevant boundary conditions and it is shown that results are consistent with measured data obtained from literature. Then we focus on the obtaining the pressure field from the velocity field. The presented method provides more accurate pressure approximation than commonly used Pressure Poisson Equation. The last chapter of the thesis is dedicated to Nitsche's method for treating slip boundary...

Meshless methods provide a highly continuous approximation field, convenient for thin structures like shells. Nevertheless, the lack of Kronecker Delta property makes the formulation of essential boundary conditions not straightforward, as the trial and test fields cannot be tailored to boundary values. Similar problem arise when different approximation regions must be joined, in a multi-region problem, such as kinks, folds or joints. This work presents three approaches to impose both kinematic conditions: the well known Lagrange Multiplier method, used since the beginning of the Element Free Galerkin method; a pure penalty approach; and the recently rediscovered alternative of Nitsche\'s Method. We use the EFG discretization technique for thick Reissner-Mindlin shells and adapt the weak form as to separate displacement and rotational degrees of freedom and obtain suitable and separate stabilization parameters. This approach enables the modeling of discontinuous shells and local refinement on multi-region problems. / Métodos sem malha geram campos de aproximação com alta continuidade, convenientes para estruturas finas como cascas. No entanto, a ausência da propriedade de Delta de Kronecker dificulta a formulação de condições essenciais de contorno, já que os campos de aproximação e teste não podem ser moldados aos valores de contorno. Um problema similar aparece quando diferentes regiões de aproximação precisam ser juntadas em um problema multi-regiões como dobras, vincos ou junções. Este trabalho apresenta três métodos de imposição ambas condições cinemáticas: o já conhecido método dos multiplicadores de Lagrange, usado desde o começo do método de Galekin sem elementos (EFG); uma abordagem de penalidade pura; e o recentemente redescoberto método de Nitsche. Nós usamos a técnica de discretização com EFG para cascas espessas de Reissner-Mindlin e adaptamos a forma fraca de forma a separar graus de liberdade de deslocamento e rotação e obter coeficientes de estabilização diferentes e apropriados. Essa abordagem permite a modelagem de cascas discontínuas e o refinamento local em problemas multi-regiões.