We use a bead-spring model simulated by Brownian Dynamics (BD) with hydrodynamic interactions represented by the Rotne-Prager tensor, or simulated by Stochastic Rotation Dynamics (SRD) to study the dynamics of a wide range of deformable micro-objects, including 1): motile bacteria, 2): deformable colloids, 3): bio-polymers, and 4): polymers in microchannels. 1. For motile bacteria, we use BD simulations to reproduce the experimentally observed behaviors of E. coli, namely, a three-dimensional random-walk trajectory in run-and-tumble motion and steady clockwise swimming near a wall. We find that the polymorphic transformation of a flagellum in a tumble facilitates the reorientation of the bacterium, and that the time-averaged flow field near a cell in a run has double-layered helical streamlines, with a time-dependent flow magnitude large enough to affect the transport of surrounding chemoattractants. 2. We find using BD simulations that deformable colloids with anisotropic rigidity, represented in our model as tetragons of four beads connected by a combination of six hard and soft springs, can be deformed into chiral shapes by a shearing flow and as a results migrate in the vorticity direction of the shear flow. 3. We find using BD simulations that the electrophoretic mobility of polyelectrolytes, such as DNA molecules, increases with DNA stretch, and that this increase is more pronounced for folded conformations than for unfolded ones. 4. We find using SRD simulations that DNA in a thin-gap Poiseuille flow between two parallel planes tends to concentrate near the center of the channel in agreement with experimental results.