I discuss two ongoing research programs concerning stochastic microphysical models in biology. First, in joint work with Grigorios Pavliotis (Imperial College) and Juan Latorre, we apply the methods of homogenization theory to compute transport properties for mathematical models (Brownian motors) of molecular motors in cells. The objective is to ascertain how the design properties of the motor affect its function. Secondly, in joint work with Shekhar Garde and Adnan Khan, we explore a simple stochastic model for the behavior of water molecules near a solute surface which has the potential for improving substantially upon Brownian dynamics models more conventionally used in engineering applications. We use exactly solvable mathematical models as a testbed for addressing some basic data-driven parameterization issues.