This invention provides a composition matter comprising rare earth-doped up-conversion nanoparticles (UCNPs) encapsulated with a silica shell. In one embodiment, a photosensitizer is incorporated into the silica shell. In another embodiment, the composition further comprises a targeting molecule. In still another embodiment, a small interfering RNA (siRNA) molecule is also attached to the silica shell with the targeting molecule. The invention further provides methods for synthesizing such compositions and for using them in therapeutic and diagnostic applications. These applications use infrared or near infrared activation to excite the UCNPs.