As technological advances allow us to fabricate smaller autonomous self-propelled devices, it is clear that at some point directed propulsion could not come from pre-specified deterministic periodic deformation of the swimmer's body and we need to develop strategies for extracting a net directed motion from a series of random transitions in the conformation space of the swimmer. We present a theoretical formulation for describing the 'stochastic motor' that drives the motion of low Reynolds number swimmers based on this concept, and use it to study the propulsion of a simple low Reynolds number swimmer, namely, the three-sphere swimmer model. When the detailed balanced is broken and the motor is driven out of equilibrium, it can propel the swimmer in the required direction. The formulation can be used to study optimal design strategies for molecular scale low Reynolds number swimmers
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