  In molecular communications, the direct detection of signaling molecules may
be challenging due to a lack of suitable sensors and interference in the
environment. Motivated by research in molecular biology, we investigate an
indirect detection mechanism using chemical reactions between the signaling
molecules and a molecular probe to produce an easy-to-measure product at the
receiver. We consider two implementations of the proposed detection mechanism,
i.e., unrestricted probe movement and probes restricted to a volume around the
receiver. The reaction-diffusion equations describing the concentrations of the
reactant and product molecules in the system are non-linear and coupled, and
cannot be solved in closed form. Therefore, we develop an efficient iterative
algorithm by discretizing the time variable and solving for the space variables
of the equations in each time step. Our results show that the concentrations of
the product molecules and the signalling molecules share a similar
characteristic over time, i.e., a single peak and a long tail. The peak and
tail values of the product molecule concentration can be controlled by choosing
probes with suitable parameters. By carefully choosing the molecular probe and
optimizing the decision threshold, the BER can be improved significantly and
outperform that of a direct detection system.
