Abstract: Swimmers on the microscopic scale face many challenges. Examples include bacteria that use chemotaxis to obtain food, or spermatozoa that try to win a race to fertilize an egg. One major issue at these small scales is to move efficiently in the presence of Brownian noise exhibited by the surrounding molecular fluid. In addition, hydrodynamic effects play an important role and influence interactions between the swimmers and nearby surfaces. Here, we use a novel particle-based fluid simulation technique, known as Stochastic Rotation Dynamics (SRD), to study swimming at micron-scales. This approach solves the underlying thermo-hydrodynamic equations by providing a "hydrodynamic heat bath" which incorporates thermal fluctuations and provides the correct hydrodynamic interactions between embedded objects. We also use state of the art Graphics Processing Units (GPUs) to improve the performance of our simulations. In this talk, I will present case studies from two swimmers: the minimalistic Purcell swimmer, and human sperm. Our results have implications for nano- to micron-scale systems involving transport, ranging from biology to robotics. Particularly, in the case of the human sperm, our multi-scale modeling helps address a major clinical challenge, and aids in the design of optimized micro-fluidic sorting devices to select and sort sperm for in vitro fertilization (IVF).