Methods, systems, and computer readable media for data analysis and inference of particle diffusion in mucus barriers and generic permeable biomaterials are disclosed. According to one aspect, the subject matter described herein includes a method for data analysis and inference of particle diffusion in target materials, such as mucus barriers, or their simulants. The method includes collecting experimental data of observed particle movement through samples of a target material or simulant (“the target”), analyzing the collected data to determine the stochastic diffusive process that is being observed for particular particles in the particular sample, using one or more of the observed stochastic diffusive processes to simulate the diffusion of particles through layers of the target of various thicknesses, using the simulation results to determine how passage time scales according to thickness of the target, and verifying the simulation results.