A non-boundary-conforming formulation for simulating transitional and turbulent flows with complex geometries and dynamically moving boundaries on fixed orthogonal grids is developed. The underlying finite-difference solver for the filtered incompressible Navier-Stokes equations in both Cartesian and cylindrical coordinates is based on a second-order fractional step method on staggered grid. To satisfy the boundary conditions on an arbitrary immersed interface, the velocity field at the grid points near the interface is reconstructed locally without smearing the sharp interface. The complications caused by the Eulerian grid points emerging from a moving solid body into the fluid phase are treated with a novel ``field-extension'' strategy. To treat the two-way interactions between the fluid and structure, a strong coupling scheme based on Hamming's fourth-order predictor-corrector method has been developed. The fluid and the structure are treated as elements of a single dynamical system, and all of the governing equations are integrated simultaneously, and iteratively in the time-domain.

A variety of two and three-dimensional fluid-structure interaction problems of increasing complexity have been considered to demonstrate the accuracy and the range of applicability of the method. In particular, forced vibrations of a rigid circular cylinder including the harmonic in-line vibrations in a quiescent fluid and the transverse vibrations in a free-stream, and the vortex-induced vibrations of an elastic cylinder with one and two degrees of freedom in a free-stream are presented and compared with reference simulations and experiments. Three-dimensional DNS and LES of fluid flows involving stationary complex geometries include the flow past a sphere at $Re=50 \sim 1,000$, the transitional flow past an airfoil with a $10^\circ$ attack angle at $Re=10,000$. Then, the turbulent flow over a traveling wavy wall at $Re=10,170$ are simulated are compared with the detailed DNS using body-fitted grid in the literature. Finally, the simulation of the transitional flow past a prosthetic mechanical heart valve with moving leaflets at $Re=4,000$ has been performed. All results are in good agreement with the available reference data.