This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or magnetism. The dynamics of the diffusion process are modeled by multi-dimensional transfer functions in a spatio-temporal frequency domain. Realistic boundary conditions are incorporated by the design of a feedback loop. The result is a discretetime semi-analytical model for the particle concentration in the channel. The model is validated by comparison to particlebased simulations. These numerical experiments reveal that the particle concentration of the proposed semi-analytical model and the particle-based model are in excellent agreement. The analytical form of the proposed solution provides several benefits over purely numerical models, e.g. high flexibility, existence of low run-time algorithms, extendability to several kinds of boundary conditions, and analytical connection to parameters from communication theory.