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In this work we aim at the description, study and numerical investigation of the fluid-structure interaction (FSI) problem applied to hemodynamics. The FSI model considered consists of the Navier-Stokes equations on moving domains modeling blood as a viscous incompressible fluid and the elasticity equation modeling the arterial wall. The fluid equations are derived in an arbitrary Lagrangian-Eulerian (ALE) frame of reference. Several existing formulations and discretizations are discussed, providing a state of the art on the subject. The main new contributions and advancements consist of: A description of the Newton method for FSI-ALE, with details on the implementation of the shape derivatives block assembling, considerations about parallel performance, the analytic derivation of the derivative terms for different formulations (conservative or not) and for different types of boundary conditions. The implementation and analysis of a new category of preconditioners for FSI (applicable also to more general coupled problems). The framework set up is general and extensible. The proposed preconditioners allow, in particular, a separate treatment of each field, using a different preconditioning strategy in each case. An estimate for the condition number of the preconditioned system is proposed, showing how preconditioners of this type depend on the coupling, and explaining the good performance they exhibit when increasing the number of processors. The improvement of the free (distributed under LGPL licence) parallel finite elements library LifeV. Most of the methods described have been implemented within this library during the period of this PhD and all the numerical tests reported were run using this framework. The simulation of clinical cases with patient-specific data and geometry, the comparison on simulations of physiological interest between different models (rigid, FSI, 1D), discretizations and methods to solve the nonlinear system. A methodology to obtain patient-specific FSI simulations starting from the raw medical data and using a set of free software tools is described. This pipeline from imaging to simulation can help medical doctors in diagnosis and decision making, and in understanding the implication of indicators such as the wall shear stress in the pathogenesis.